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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/class-use/MapReduceRunner.html b/halvade/dist/javadoc/be/ugent/intec/halvade/class-use/MapReduceRunner.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html
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-<div class="subTitle">be.ugent.intec.halvade.hadoop.datatypes</div>
-<h2 title="Class ChromosomeRegion" class="title">Class ChromosomeRegion</h2>
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-<li>java.lang.Object</li>
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-<pre>public class <span class="strong">ChromosomeRegion</span>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/datatypes/class-use/ChromosomeRegion.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/datatypes/class-use/ChromosomeRegion.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/datatypes/package-frame.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/datatypes/package-frame.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineMapper.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineMapper.html
deleted file mode 100644
index 46f58c7..0000000
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html
+++ /dev/null
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineMapper.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineMapper.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/AlignedBamMapper.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/AlignedBamMapper.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/BWAAlnMapper.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/BWAAlnMapper.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/BWAMemMapper.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/BWAMemMapper.html
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+++ /dev/null
@@ -1,116 +0,0 @@
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/BamMergeReducer.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/BamMergeReducer.html
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+++ /dev/null
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/Bowtie2Mapper.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/Bowtie2Mapper.html
deleted file mode 100644
index 4c9dd1a..0000000
--- a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/Bowtie2Mapper.html
+++ /dev/null
@@ -1,116 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/CountReadsReducer.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/CountReadsReducer.html
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index 5e32399..0000000
--- a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/CountReadsReducer.html
+++ /dev/null
@@ -1,116 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<li class="navBarCell1Rev">Use</li>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/Cushaw2Mapper.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/Cushaw2Mapper.html
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index 34b48c2..0000000
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/DnaGATKReducer.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/DnaGATKReducer.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/GATKReducer.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/GATKReducer.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/HTSeqCombineMapper.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/HTSeqCombineMapper.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/HTSeqCombineReducer.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/HTSeqCombineReducer.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/HalvadeCounters.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/HalvadeCounters.html
deleted file mode 100644
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-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="#be.ugent.intec.halvade.hadoop.mapreduce">be.ugent.intec.halvade.hadoop.mapreduce</a></td>
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-<th class="colLast" scope="col">Method and Description</th>
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-<td class="colFirst"><code>static <a href="../../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeCounters.html" title="enum in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeCounters</a></code></td>
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-<td class="colFirst"><code>static boolean</code></td>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/HalvadeMapper.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/HalvadeMapper.html
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/HalvadeMapper.html
+++ /dev/null
@@ -1,172 +0,0 @@
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-        parent.document.title="Uses of Class be.ugent.intec.halvade.hadoop.mapreduce.HalvadeMapper";
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/RebuildStarGenomeReducer.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/RebuildStarGenomeReducer.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/RnaGATKReducer.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/RnaGATKReducer.html
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@@ -1,116 +0,0 @@
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/StarAlignPassXMapper.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/StarAlignPassXMapper.html
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/StarAlignPassXMapper.html
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@@ -1,116 +0,0 @@
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/VCFCombineMapper.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/VCFCombineMapper.html
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/VCFCombineMapper.html
+++ /dev/null
@@ -1,116 +0,0 @@
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/VCFCombineReducer.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/VCFCombineReducer.html
deleted file mode 100644
index 9a304e3..0000000
--- a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/mapreduce/class-use/VCFCombineReducer.html
+++ /dev/null
@@ -1,116 +0,0 @@
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/ChrRgGroupingComparator.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/ChrRgGroupingComparator.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/ChrRgPartitioner.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/ChrRgPartitioner.html
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-</div>
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-<li>java.lang.Object</li>
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-<li>org.apache.hadoop.mapreduce.Partitioner&lt;<a href="../../../../../../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a>,org.seqdoop.hadoop_bam.SAMRecordWritable&gt;</li>
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-<td class="colFirst"><code>int</code></td>
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-<dt><strong>Specified by:</strong></dt>
-<dd><code>getPartition</code>&nbsp;in class&nbsp;<code>org.apache.hadoop.mapreduce.Partitioner&lt;<a href="../../../../../../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a>,org.seqdoop.hadoop_bam.SAMRecordWritable&gt;</code></dd>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/ChrRgSortComparator.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/ChrRgSortComparator.html
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-<meta name="date" content="2016-01-23">
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-<div class="subTitle">be.ugent.intec.halvade.hadoop.partitioners</div>
-<h2 title="Class ChrRgSortComparator" class="title">Class ChrRgSortComparator</h2>
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-<pre>public class <span class="strong">ChrRgSortComparator</span>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/class-use/ChrRgGroupingComparator.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/class-use/ChrRgGroupingComparator.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/class-use/ChrRgPartitioner.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/class-use/ChrRgPartitioner.html
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@@ -1,116 +0,0 @@
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/class-use/ChrRgSortComparator.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/class-use/ChrRgSortComparator.html
deleted file mode 100644
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+++ /dev/null
@@ -1,116 +0,0 @@
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/class-use/GenomeSJGroupingComparator.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/class-use/GenomeSJGroupingComparator.html
deleted file mode 100644
index 2138044..0000000
--- a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/class-use/GenomeSJGroupingComparator.html
+++ /dev/null
@@ -1,116 +0,0 @@
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/class-use/GenomeSJSortComparator.html b/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/class-use/GenomeSJSortComparator.html
deleted file mode 100644
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/hadoop/partitioners/class-use/GenomeSJSortComparator.html
+++ /dev/null
@@ -1,116 +0,0 @@
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/AlignerInstance.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/AlignerInstance.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/Bowtie2Instance.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/Bowtie2Instance.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/PreprocessingTools.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/PreprocessingTools.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/AlignerInstance.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/AlignerInstance.html
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-<li><a href="../../../../../../deprecated-list.html">Deprecated</a></li>
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-<h2 title="Uses of Class be.ugent.intec.halvade.tools.AlignerInstance" class="title">Uses of Class<br>be.ugent.intec.halvade.tools.AlignerInstance</h2>
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-<tr>
-<th class="colFirst" scope="col">Package</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="#be.ugent.intec.halvade.hadoop.mapreduce">be.ugent.intec.halvade.hadoop.mapreduce</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="#be.ugent.intec.halvade.tools">be.ugent.intec.halvade.tools</a></td>
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-<th class="colFirst" scope="col">Modifier and Type</th>
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-<td class="colFirst"><code>protected <a href="../../../../../../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></code></td>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/BWAAlnInstance.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/BWAAlnInstance.html
deleted file mode 100644
index c90b6f2..0000000
--- a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/BWAAlnInstance.html
+++ /dev/null
@@ -1,157 +0,0 @@
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-<!-- Generated by javadoc (version 1.7.0_91) on Sat Jan 23 21:38:55 CET 2016 -->
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-<title>Uses of Class be.ugent.intec.halvade.tools.BWAAlnInstance</title>
-<meta name="date" content="2016-01-23">
-<link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
-</head>
-<body>
-<script type="text/javascript"><!--
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-<div>JavaScript is disabled on your browser.</div>
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-<!-- ========= START OF TOP NAVBAR ======= -->
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-<!--   -->
-</a><a href="#skip-navbar_top" title="Skip navigation links"></a><a name="navbar_top_firstrow">
-<!--   -->
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-<li><a href="../../../../../../overview-summary.html">Overview</a></li>
-<li><a href="../package-summary.html">Package</a></li>
-<li><a href="../../../../../../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">Class</a></li>
-<li class="navBarCell1Rev">Use</li>
-<li><a href="../../../../../../overview-tree.html">Tree</a></li>
-<li><a href="../../../../../../deprecated-list.html">Deprecated</a></li>
-<li><a href="../../../../../../index-files/index-1.html">Index</a></li>
-<li><a href="../../../../../../help-doc.html">Help</a></li>
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-<li>Prev</li>
-<li>Next</li>
-</ul>
-<ul class="navList">
-<li><a href="../../../../../../index.html?be/ugent/intec/halvade/tools/class-use/BWAAlnInstance.html" target="_top">Frames</a></li>
-<li><a href="BWAAlnInstance.html" target="_top">No Frames</a></li>
-</ul>
-<ul class="navList" id="allclasses_navbar_top">
-<li><a href="../../../../../../allclasses-noframe.html">All Classes</a></li>
-</ul>
-<div>
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-<!-- ========= END OF TOP NAVBAR ========= -->
-<div class="header">
-<h2 title="Uses of Class be.ugent.intec.halvade.tools.BWAAlnInstance" class="title">Uses of Class<br>be.ugent.intec.halvade.tools.BWAAlnInstance</h2>
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-<caption><span>Packages that use <a href="../../../../../../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">BWAAlnInstance</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Package</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="#be.ugent.intec.halvade.tools">be.ugent.intec.halvade.tools</a></td>
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-<h3>Uses of <a href="../../../../../../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">BWAAlnInstance</a> in <a href="../../../../../../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></h3>
-<table border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
-<caption><span>Methods in <a href="../../../../../../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a> that return <a href="../../../../../../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">BWAAlnInstance</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><code>static <a href="../../../../../../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">BWAAlnInstance</a></code></td>
-<td class="colLast"><span class="strong">BWAAlnInstance.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/tools/BWAAlnInstance.html#getBWAInstance(org.apache.hadoop.mapreduce.Mapper.Context,%20java.lang.String)">getBWAInstance</a></strong>(org.apache.hadoop.mapreduce.Mapper.Context&nbsp;context,
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->
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-<li><a href="../package-summary.html">Package</a></li>
-<li><a href="../../../../../../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">Class</a></li>
-<li class="navBarCell1Rev">Use</li>
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-<li>Next</li>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/BWAMemInstance.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/BWAMemInstance.html
deleted file mode 100644
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/BWAMemInstance.html
+++ /dev/null
@@ -1,157 +0,0 @@
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-<!-- Generated by javadoc (version 1.7.0_91) on Sat Jan 23 21:38:55 CET 2016 -->
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-<title>Uses of Class be.ugent.intec.halvade.tools.BWAMemInstance</title>
-<meta name="date" content="2016-01-23">
-<link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
-</head>
-<body>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/Bowtie2Instance.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/Bowtie2Instance.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/Cushaw2Instance.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/Cushaw2Instance.html
deleted file mode 100644
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/Cushaw2Instance.html
+++ /dev/null
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-<title>Uses of Class be.ugent.intec.halvade.tools.Cushaw2Instance</title>
-<meta name="date" content="2016-01-23">
-<link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
-</head>
-<body>
-<script type="text/javascript"><!--
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-<caption><span>Methods in <a href="../../../../../../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a> that return <a href="../../../../../../be/ugent/intec/halvade/tools/Cushaw2Instance.html" title="class in be.ugent.intec.halvade.tools">Cushaw2Instance</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
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-<tr class="altColor">
-<td class="colFirst"><code>static <a href="../../../../../../be/ugent/intec/halvade/tools/Cushaw2Instance.html" title="class in be.ugent.intec.halvade.tools">Cushaw2Instance</a></code></td>
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-<li><a href="../../../../../../be/ugent/intec/halvade/tools/Cushaw2Instance.html" title="class in be.ugent.intec.halvade.tools">Class</a></li>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/DummyAlignerInstance.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/DummyAlignerInstance.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/PreprocessingTools.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/PreprocessingTools.html
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-<link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
-</head>
-<body>
-<script type="text/javascript"><!--
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-<li><a href="../../../../../../deprecated-list.html">Deprecated</a></li>
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-<h2 title="Uses of Class be.ugent.intec.halvade.tools.PreprocessingTools" class="title">Uses of Class<br>be.ugent.intec.halvade.tools.PreprocessingTools</h2>
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-<caption><span>Packages that use <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colFirst" scope="col">Package</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="#be.ugent.intec.halvade.hadoop.mapreduce">be.ugent.intec.halvade.hadoop.mapreduce</a></td>
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-<table border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
-<caption><span>Methods in <a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a> with parameters of type <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colFirst" scope="col">Modifier and Type</th>
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-<tr class="altColor">
-<td class="colFirst"><code>protected void</code></td>
-<td class="colLast"><span class="strong">GATKReducer.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#baseQualityScoreRecalibration(org.apache.hadoop.mapreduce.Reducer.Context,%20java.lang.String,%20be.ugent.intec.halvade.utils.ChromosomeRange,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.tools.GATKTools,%20java.lang.String,%20java.lang.String)">baseQualityScoreRecalibration</a></strong>(org.apache.hadoop.mapreduce.Reducer.Context&nbsp;context,
-                             java.lang.String&nbsp;region,
-                             <a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange</a>&nbsp;r,
-                             <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a>&nbsp;tools,
-                             <a href="../../../../../../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a>&nbsp;gatk,
-                             java.lang.String&nbsp;input,
-                             java.lang.String&nbsp;output)</code>&nbsp;</td>
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-<td class="colFirst"><code>protected void</code></td>
-<td class="colLast"><span class="strong">GATKReducer.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#elPrepPreprocess(org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.utils.SAMRecordIterator,%20java.lang.String)">elPrepPreprocess</a></strong>(org.apache.hadoop.mapreduce.Reducer.Context&nbsp;context,
-                <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a>&nbsp;tools,
-                <a href="../../../../../../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a>&nbsp;input,
-                java.lang.String&nbsp;output)</code>&nbsp;</td>
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-<tr class="altColor">
-<td class="colFirst"><code>protected java.lang.String</code></td>
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-              <a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange</a>&nbsp;r,
-              <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a>&nbsp;tools,
-              java.lang.String&nbsp;region)</code>&nbsp;</td>
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-<tr class="rowColor">
-<td class="colFirst"><code>protected void</code></td>
-<td class="colLast"><span class="strong">GATKReducer.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#PicardPreprocess(org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.utils.SAMRecordIterator,%20java.lang.String)">PicardPreprocess</a></strong>(org.apache.hadoop.mapreduce.Reducer.Context&nbsp;context,
-                <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a>&nbsp;tools,
-                <a href="../../../../../../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a>&nbsp;input,
-                java.lang.String&nbsp;output)</code>&nbsp;</td>
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-<tr class="altColor">
-<td class="colFirst"><code>protected void</code></td>
-<td class="colLast"><span class="strong">DnaGATKReducer.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/DnaGATKReducer.html#processAlignments(java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.tools.GATKTools)">processAlignments</a></strong>(java.lang.Iterable&lt;org.seqdoop.hadoop_bam.SAMRecordWritable&gt;&nbsp;values,
-                 org.apache.hadoop.mapreduce.Reducer.Context&nbsp;context,
-                 <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a>&nbsp;tools,
-                 <a href="../../../../../../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a>&nbsp;gatk)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>protected abstract void</code></td>
-<td class="colLast"><span class="strong">GATKReducer.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#processAlignments(java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.tools.GATKTools)">processAlignments</a></strong>(java.lang.Iterable&lt;org.seqdoop.hadoop_bam.SAMRecordWritable&gt;&nbsp;values,
-                 org.apache.hadoop.mapreduce.Reducer.Context&nbsp;context,
-                 <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a>&nbsp;tools,
-                 <a href="../../../../../../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a>&nbsp;gatk)</code>&nbsp;</td>
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-<td class="colFirst"><code>protected void</code></td>
-<td class="colLast"><span class="strong">RnaGATKReducer.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/RnaGATKReducer.html#processAlignments(java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.tools.GATKTools)">processAlignments</a></strong>(java.lang.Iterable&lt;org.seqdoop.hadoop_bam.SAMRecordWritable&gt;&nbsp;values,
-                 org.apache.hadoop.mapreduce.Reducer.Context&nbsp;context,
-                 <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a>&nbsp;tools,
-                 <a href="../../../../../../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a>&nbsp;gatk)</code>&nbsp;</td>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/ProcessException.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/ProcessException.html
deleted file mode 100644
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/ProcessException.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/QualityEncoding.QENCODING.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/QualityEncoding.QENCODING.html
deleted file mode 100644
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/QualityEncoding.QENCODING.html
+++ /dev/null
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-<!-- Generated by javadoc (version 1.7.0_91) on Sat Jan 23 21:38:55 CET 2016 -->
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<title>Uses of Class be.ugent.intec.halvade.tools.QualityEncoding.QENCODING</title>
-<meta name="date" content="2016-01-23">
-<link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
-</head>
-<body>
-<script type="text/javascript"><!--
-    if (location.href.indexOf('is-external=true') == -1) {
-        parent.document.title="Uses of Class be.ugent.intec.halvade.tools.QualityEncoding.QENCODING";
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-//-->
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-<li class="navBarCell1Rev">Use</li>
-<li><a href="../../../../../../overview-tree.html">Tree</a></li>
-<li><a href="../../../../../../deprecated-list.html">Deprecated</a></li>
-<li><a href="../../../../../../index-files/index-1.html">Index</a></li>
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-<caption><span>Packages that use <a href="../../../../../../be/ugent/intec/halvade/tools/QualityEncoding.QENCODING.html" title="enum in be.ugent.intec.halvade.tools">QualityEncoding.QENCODING</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<table border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
-<caption><span>Methods in <a href="../../../../../../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a> that return <a href="../../../../../../be/ugent/intec/halvade/tools/QualityEncoding.QENCODING.html" title="enum in be.ugent.intec.halvade.tools">QualityEncoding.QENCODING</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colFirst" scope="col">Modifier and Type</th>
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-<tr class="altColor">
-<td class="colFirst"><code>static <a href="../../../../../../be/ugent/intec/halvade/tools/QualityEncoding.QENCODING.html" title="enum in be.ugent.intec.halvade.tools">QualityEncoding.QENCODING</a></code></td>
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-<td class="colFirst"><code>static <a href="../../../../../../be/ugent/intec/halvade/tools/QualityEncoding.QENCODING.html" title="enum in be.ugent.intec.halvade.tools">QualityEncoding.QENCODING</a></code></td>
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-<div class="block">Returns the enum constant of this type with the specified name.</div>
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-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static <a href="../../../../../../be/ugent/intec/halvade/tools/QualityEncoding.QENCODING.html" title="enum in be.ugent.intec.halvade.tools">QualityEncoding.QENCODING</a>[]</code></td>
-<td class="colLast"><span class="strong">QualityEncoding.QENCODING.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/tools/QualityEncoding.QENCODING.html#values()">values</a></strong>()</code>
-<div class="block">Returns an array containing the constants of this enum type, in
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-<li><a href="../../../../../../be/ugent/intec/halvade/tools/QualityEncoding.QENCODING.html" title="enum in be.ugent.intec.halvade.tools">Class</a></li>
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-<li><a href="../../../../../../deprecated-list.html">Deprecated</a></li>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/QualityEncoding.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/QualityEncoding.html
deleted file mode 100644
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/QualityEncoding.html
+++ /dev/null
@@ -1,116 +0,0 @@
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-<!-- Generated by javadoc (version 1.7.0_91) on Sat Jan 23 21:38:55 CET 2016 -->
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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-<li><a href="../../../../../../be/ugent/intec/halvade/tools/QualityEncoding.html" title="class in be.ugent.intec.halvade.tools">Class</a></li>
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-</div>
-<div class="classUseContainer">No usage of be.ugent.intec.halvade.tools.QualityEncoding</div>
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
-<div class="bottomNav"><a name="navbar_bottom">
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-<li><a href="../../../../../../be/ugent/intec/halvade/tools/QualityEncoding.html" title="class in be.ugent.intec.halvade.tools">Class</a></li>
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-<li><a href="QualityEncoding.html" target="_top">No Frames</a></li>
-</ul>
-<ul class="navList" id="allclasses_navbar_bottom">
-<li><a href="../../../../../../allclasses-noframe.html">All Classes</a></li>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/QualityException.html b/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/QualityException.html
deleted file mode 100644
index 0c22ee5..0000000
--- a/halvade/dist/javadoc/be/ugent/intec/halvade/tools/class-use/QualityException.html
+++ /dev/null
@@ -1,263 +0,0 @@
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-<head>
-<!-- Generated by javadoc (version 1.7.0_91) on Sat Jan 23 21:38:55 CET 2016 -->
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<title>Uses of Class be.ugent.intec.halvade.tools.QualityException</title>
-<meta name="date" content="2016-01-23">
-<link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
-</head>
-<body>
-<script type="text/javascript"><!--
-    if (location.href.indexOf('is-external=true') == -1) {
-        parent.document.title="Uses of Class be.ugent.intec.halvade.tools.QualityException";
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-<noscript>
-<div>JavaScript is disabled on your browser.</div>
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-<!-- ========= START OF TOP NAVBAR ======= -->
-<div class="topNav"><a name="navbar_top">
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-<li><a href="../../../../../../be/ugent/intec/halvade/tools/QualityException.html" title="class in be.ugent.intec.halvade.tools">Class</a></li>
-<li class="navBarCell1Rev">Use</li>
-<li><a href="../../../../../../overview-tree.html">Tree</a></li>
-<li><a href="../../../../../../deprecated-list.html">Deprecated</a></li>
-<li><a href="../../../../../../index-files/index-1.html">Index</a></li>
-<li><a href="../../../../../../help-doc.html">Help</a></li>
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-<li><a href="QualityException.html" target="_top">No Frames</a></li>
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-<div>
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-<!-- ========= END OF TOP NAVBAR ========= -->
-<div class="header">
-<h2 title="Uses of Class be.ugent.intec.halvade.tools.QualityException" class="title">Uses of Class<br>be.ugent.intec.halvade.tools.QualityException</h2>
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-<ul class="blockList">
-<li class="blockList">
-<table border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
-<caption><span>Packages that use <a href="../../../../../../be/ugent/intec/halvade/tools/QualityException.html" title="class in be.ugent.intec.halvade.tools">QualityException</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Package</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="#be.ugent.intec.halvade.hadoop.mapreduce">be.ugent.intec.halvade.hadoop.mapreduce</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="#be.ugent.intec.halvade.tools">be.ugent.intec.halvade.tools</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="#be.ugent.intec.halvade.utils">be.ugent.intec.halvade.utils</a></td>
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-<h3>Uses of <a href="../../../../../../be/ugent/intec/halvade/tools/QualityException.html" title="class in be.ugent.intec.halvade.tools">QualityException</a> in <a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></h3>
-<table border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
-<caption><span>Methods in <a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a> that throw <a href="../../../../../../be/ugent/intec/halvade/tools/QualityException.html" title="class in be.ugent.intec.halvade.tools">QualityException</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><code>protected void</code></td>
-<td class="colLast"><span class="strong">GATKReducer.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#elPrepPreprocess(org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.utils.SAMRecordIterator,%20java.lang.String)">elPrepPreprocess</a></strong>(org.apache.hadoop.mapreduce.Reducer.Context&nbsp;context,
-                <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a>&nbsp;tools,
-                <a href="../../../../../../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a>&nbsp;input,
-                java.lang.String&nbsp;output)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>protected void</code></td>
-<td class="colLast"><span class="strong">GATKReducer.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#PicardPreprocess(org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.utils.SAMRecordIterator,%20java.lang.String)">PicardPreprocess</a></strong>(org.apache.hadoop.mapreduce.Reducer.Context&nbsp;context,
-                <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a>&nbsp;tools,
-                <a href="../../../../../../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a>&nbsp;input,
-                java.lang.String&nbsp;output)</code>&nbsp;</td>
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-                 org.apache.hadoop.mapreduce.Reducer.Context&nbsp;context,
-                 <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a>&nbsp;tools,
-                 <a href="../../../../../../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a>&nbsp;gatk)</code>&nbsp;</td>
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-<tr class="rowColor">
-<td class="colFirst"><code>protected abstract void</code></td>
-<td class="colLast"><span class="strong">GATKReducer.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#processAlignments(java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.tools.GATKTools)">processAlignments</a></strong>(java.lang.Iterable&lt;org.seqdoop.hadoop_bam.SAMRecordWritable&gt;&nbsp;values,
-                 org.apache.hadoop.mapreduce.Reducer.Context&nbsp;context,
-                 <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a>&nbsp;tools,
-                 <a href="../../../../../../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a>&nbsp;gatk)</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>protected void</code></td>
-<td class="colLast"><span class="strong">RnaGATKReducer.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/hadoop/mapreduce/RnaGATKReducer.html#processAlignments(java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.tools.GATKTools)">processAlignments</a></strong>(java.lang.Iterable&lt;org.seqdoop.hadoop_bam.SAMRecordWritable&gt;&nbsp;values,
-                 org.apache.hadoop.mapreduce.Reducer.Context&nbsp;context,
-                 <a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a>&nbsp;tools,
-                 <a href="../../../../../../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a>&nbsp;gatk)</code>&nbsp;</td>
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-<table border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
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-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><span class="strong">PreprocessingTools.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/tools/PreprocessingTools.html#callElPrep(java.lang.String,%20java.lang.String,%20java.lang.String,%20int,%20be.ugent.intec.halvade.utils.SAMRecordIterator,%20htsjdk.samtools.SAMFileHeader,%20java.lang.String,%20boolean,%20java.lang.String)">callElPrep</a></strong>(java.lang.String&nbsp;input,
-          java.lang.String&nbsp;output,
-          java.lang.String&nbsp;rg,
-          int&nbsp;threads,
-          <a href="../../../../../../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a>&nbsp;SAMit,
-          htsjdk.samtools.SAMFileHeader&nbsp;header,
-          java.lang.String&nbsp;dictFile,
-          boolean&nbsp;updateRG,
-          java.lang.String&nbsp;RGID)</code>&nbsp;</td>
-</tr>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegionComparator.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegionComparator.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/HalvadeFileUtils.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/HalvadeFileUtils.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeRange.Range.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeRange.Range.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeRange.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeRange.html
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-<td class="colFirst"><code>protected void</code></td>
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-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange</a></code></td>
-<td class="colLast"><span class="strong">SAMRecordIterator.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/utils/SAMRecordIterator.html#getChromosomeRange()">getChromosomeRange</a></strong>()</code>&nbsp;</td>
-</tr>
-</tbody>
-</table>
-<table border="0" cellpadding="3" cellspacing="0" summary="Use table, listing constructors, and an explanation">
-<caption><span>Constructors in <a href="../../../../../../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a> with parameters of type <a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colLast"><code><strong><a href="../../../../../../be/ugent/intec/halvade/utils/SAMRecordIterator.html#SAMRecordIterator(java.util.Iterator,%20htsjdk.samtools.SAMFileHeader,%20be.ugent.intec.halvade.utils.ChromosomeRange)">SAMRecordIterator</a></strong>(java.util.Iterator&lt;org.seqdoop.hadoop_bam.SAMRecordWritable&gt;&nbsp;it,
-                 htsjdk.samtools.SAMFileHeader&nbsp;header,
-                 <a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange</a>&nbsp;r)</code>&nbsp;</td>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.BedRegion.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.BedRegion.html
deleted file mode 100644
index a816a0a..0000000
--- a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.BedRegion.html
+++ /dev/null
@@ -1,201 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
-<head>
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-<meta name="date" content="2016-01-23">
-<link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
-</head>
-<body>
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-    if (location.href.indexOf('is-external=true') == -1) {
-        parent.document.title="Uses of Class be.ugent.intec.halvade.utils.ChromosomeSplitter.BedRegion";
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-<h2 title="Uses of Class be.ugent.intec.halvade.utils.ChromosomeSplitter.BedRegion" class="title">Uses of Class<br>be.ugent.intec.halvade.utils.ChromosomeSplitter.BedRegion</h2>
-</div>
-<div class="classUseContainer">
-<ul class="blockList">
-<li class="blockList">
-<table border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
-<caption><span>Packages that use <a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Package</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="#be.ugent.intec.halvade.utils">be.ugent.intec.halvade.utils</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList">
-<ul class="blockList">
-<li class="blockList"><a name="be.ugent.intec.halvade.utils">
-<!--   -->
-</a>
-<h3>Uses of <a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a> in <a href="../../../../../../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></h3>
-<table border="0" cellpadding="3" cellspacing="0" summary="Use table, listing fields, and an explanation">
-<caption><span>Fields in <a href="../../../../../../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a> with type parameters of type <a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Field and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><code>protected java.util.ArrayList&lt;<a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a>&gt;</code></td>
-<td class="colLast"><span class="strong">ChromosomeSplitter.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#regions">regions</a></strong></code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>protected java.util.HashMap&lt;java.lang.String,java.util.ArrayList&lt;<a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a>&gt;&gt;</code></td>
-<td class="colLast"><span class="strong">ChromosomeSplitter.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#regionsByChrom">regionsByChrom</a></strong></code>&nbsp;</td>
-</tr>
-</tbody>
-</table>
-<table border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
-<caption><span>Methods in <a href="../../../../../../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a> that return types with arguments of type <a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><code>java.util.HashMap&lt;java.lang.String,java.util.List&lt;<a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a>&gt;&gt;</code></td>
-<td class="colLast"><span class="strong">ChromosomeSplitter.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#makeRegionListFromFile(java.lang.String)">makeRegionListFromFile</a></strong>(java.lang.String&nbsp;countsFile)</code>&nbsp;</td>
-</tr>
-</tbody>
-</table>
-<table border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
-<caption><span>Methods in <a href="../../../../../../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a> with parameters of type <a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><span class="strong">ChromosomeSplitter.BedRegionComparator.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegionComparator.html#compare(be.ugent.intec.halvade.utils.ChromosomeSplitter.BedRegion,%20be.ugent.intec.halvade.utils.ChromosomeSplitter.BedRegion)">compare</a></strong>(<a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a>&nbsp;o1,
-       <a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a>&nbsp;o2)</code>&nbsp;</td>
-</tr>
-</tbody>
-</table>
-<table border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
-<caption><span>Method parameters in <a href="../../../../../../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a> with type arguments of type <a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><span class="strong">ChromosomeSplitter.</span><code><strong><a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#getReadsPerContig(java.util.List,%20java.lang.String)">getReadsPerContig</a></strong>(java.util.List&lt;<a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a>&gt;&nbsp;list,
-                 java.lang.String&nbsp;contig)</code>&nbsp;</td>
-</tr>
-</tbody>
-</table>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
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-<li><a href="../../../../../../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">Class</a></li>
-<li class="navBarCell1Rev">Use</li>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.BedRegionComparator.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.BedRegionComparator.html
deleted file mode 100644
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.BedRegionComparator.html
+++ /dev/null
@@ -1,116 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
-<head>
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-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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-<meta name="date" content="2016-01-23">
-<link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
-</head>
-<body>
-<script type="text/javascript"><!--
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-</div>
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.KeyCountPair.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.KeyCountPair.html
deleted file mode 100644
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.KeyCountPair.html
+++ /dev/null
@@ -1,157 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
-<head>
-<!-- Generated by javadoc (version 1.7.0_91) on Sat Jan 23 21:38:55 CET 2016 -->
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<title>Uses of Class be.ugent.intec.halvade.utils.ChromosomeSplitter.KeyCountPair</title>
-<meta name="date" content="2016-01-23">
-<link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
-</head>
-<body>
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-        parent.document.title="Uses of Class be.ugent.intec.halvade.utils.ChromosomeSplitter.KeyCountPair";
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-//-->
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.KeyCountPairComparator.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.KeyCountPairComparator.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ChromosomeSplitter.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/CommandGenerator.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/CommandGenerator.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/HalvadeFileLock.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/HalvadeFileLock.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/HalvadeFileUtils.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/HalvadeFileUtils.html
deleted file mode 100644
index 18a3e2f..0000000
--- a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/HalvadeFileUtils.html
+++ /dev/null
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/Logger.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/Logger.html
deleted file mode 100644
index c04b86d..0000000
--- a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/Logger.html
+++ /dev/null
@@ -1,116 +0,0 @@
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-<meta name="date" content="2016-01-23">
-<link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ProcessBuilderWrapper.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/ProcessBuilderWrapper.html
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diff --git a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/SAMRecordIterator.html b/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/SAMRecordIterator.html
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--- a/halvade/dist/javadoc/be/ugent/intec/halvade/utils/class-use/SAMRecordIterator.html
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diff --git a/halvade/dist/javadoc/constant-values.html b/halvade/dist/javadoc/constant-values.html
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-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th scope="col">Constant Field</th>
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-<td class="colFirst"><a name="be.ugent.intec.halvade.HalvadeOptions.DEFAULT_COVERAGE">
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-<td class="colLast"><code>50.0</code></td>
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-</a><code>protected&nbsp;static&nbsp;final&nbsp;double</code></td>
-<td><code><a href="be/ugent/intec/halvade/HalvadeOptions.html#DEFAULT_COVERAGE_SIZE">DEFAULT_COVERAGE_SIZE</a></code></td>
-<td class="colLast"><code>86.0</code></td>
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diff --git a/halvade/dist/javadoc/deprecated-list.html b/halvade/dist/javadoc/deprecated-list.html
deleted file mode 100644
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-<title>Deprecated List</title>
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diff --git a/halvade/dist/javadoc/index-files/index-1.html b/halvade/dist/javadoc/index-files/index-1.html
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-<dd>&nbsp;</dd>
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-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#addToCommand(java.util.ArrayList,%20java.lang.String)">addToCommand(ArrayList&lt;String&gt;, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/AlignedBamMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">AlignedBamMapper</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/AlignedBamMapper.html#AlignedBamMapper()">AlignedBamMapper()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/AlignedBamMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">AlignedBamMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools"><span class="strong">AlignerInstance</span></a> - Class in <a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#AlignerInstance(org.apache.hadoop.mapreduce.Mapper.Context,%20java.lang.String)">AlignerInstance(Mapper.Context, String)</a></span> - Constructor for class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html#alignmentEnd">alignmentEnd</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange.Range</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html#alignmentStart">alignmentStart</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange.Range</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#alignmentTools">alignmentTools</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#ALL">ALL</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#allTasksCompleted(org.apache.hadoop.conf.Configuration)">allTasksCompleted(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html#allTasksHaveStarted">allTasksHaveStarted</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#aln">aln</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#annotateVariants(org.apache.hadoop.mapreduce.Reducer.Context,%20java.lang.String,%20be.ugent.intec.halvade.tools.GATKTools,%20java.lang.String,%20java.lang.String)">annotateVariants(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, String, GATKTools, String, String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#attemptDownloadFileFromHDFS(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20org.apache.hadoop.fs.FileSystem,%20java.lang.String,%20java.lang.String,%20int)">attemptDownloadFileFromHDFS(TaskInputOutputContext, FileSystem, String, String, int)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#attemptUploadFileToHDFS(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20org.apache.hadoop.fs.FileSystem,%20java.lang.String,%20java.lang.String,%20int)">attemptUploadFileToHDFS(TaskInputOutputContext, FileSystem, String, String, int)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-</dl>
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diff --git a/halvade/dist/javadoc/index-files/index-10.html b/halvade/dist/javadoc/index-files/index-10.html
deleted file mode 100644
index b49370b..0000000
--- a/halvade/dist/javadoc/index-files/index-10.html
+++ /dev/null
@@ -1,129 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<!--   -->
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-<h2 class="title">J</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#java">java</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#java">java</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#jobId">jobId</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#justAlign">justAlign</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#justCombine">justCombine</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-</dl>
-<a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">K</a>&nbsp;<a href="index-12.html">L</a>&nbsp;<a href="index-13.html">M</a>&nbsp;<a href="index-14.html">N</a>&nbsp;<a href="index-15.html">O</a>&nbsp;<a href="index-16.html">P</a>&nbsp;<a href="index-17.html">Q</a>&nbsp;<a href="index-18.html">R</a>&nbsp;<a href="index-19.html">S</a>&nbsp;<a href="index-20.html">T</a>&nbsp;<a href="index-21.html">U</a>&nbsp;<a href="index-22.html">V</a>&nbsp;<a href="index-23.html">W</a>&nbsp;</div>
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diff --git a/halvade/dist/javadoc/index-files/index-11.html b/halvade/dist/javadoc/index-files/index-11.html
deleted file mode 100644
index 0f3f2bb..0000000
--- a/halvade/dist/javadoc/index-files/index-11.html
+++ /dev/null
@@ -1,139 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
-<head>
-<!-- Generated by javadoc (version 1.7.0_91) on Sat Jan 23 21:38:55 CET 2016 -->
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<title>K-Index</title>
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-</head>
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-    if (location.href.indexOf('is-external=true') == -1) {
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-<!--   -->
-</a>
-<h2 class="title">K</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#keep">keep</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#keep">keep</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#keepChrSplitPairs">keepChrSplitPairs</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#keepChrSplitPairs">keepChrSplitPairs</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#keepDups">keepDups</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#keepDups">keepDups</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#keepFiles">keepFiles</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html#key">key</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPair.html#key">key</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPair.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.KeyCountPair</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#keyFactors">keyFactors</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-</dl>
-<a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">K</a>&nbsp;<a href="index-12.html">L</a>&nbsp;<a href="index-13.html">M</a>&nbsp;<a href="index-14.html">N</a>&nbsp;<a href="index-15.html">O</a>&nbsp;<a href="index-16.html">P</a>&nbsp;<a href="index-17.html">Q</a>&nbsp;<a href="index-18.html">R</a>&nbsp;<a href="index-19.html">S</a>&nbsp;<a href="index-20.html">T</a>&nbsp;<a href="index-21.html">U</a>&nbsp;<a href="index-22.html">V</a>&nbsp;<a href="index-23.html">W</a>&nbsp;</div>
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diff --git a/halvade/dist/javadoc/index-files/index-12.html b/halvade/dist/javadoc/index-files/index-12.html
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-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#lengthByContig">lengthByContig</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html#loadReference(org.apache.hadoop.mapreduce.Mapper.Context)">loadReference(Mapper&lt;LongWritable, Text, GenomeSJ, Text&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">StarAlignPassXMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#loadSharedMemoryReference(java.lang.String,%20boolean)">loadSharedMemoryReference(String, boolean)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#localRefDir">localRefDir</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#lock">lock</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#lockfile">lockfile</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/Logger.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">Logger</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Logger.html#Logger()">Logger()</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Logger.html" title="class in be.ugent.intec.halvade.utils">Logger</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#LT_FACTOR">LT_FACTOR</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-</dl>
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diff --git a/halvade/dist/javadoc/index-files/index-13.html b/halvade/dist/javadoc/index-files/index-13.html
deleted file mode 100644
index bd3deeb..0000000
--- a/halvade/dist/javadoc/index-files/index-13.html
+++ /dev/null
@@ -1,183 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/Halvade.html#main(java.lang.String[])">main(String[])</a></span> - Static method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/Halvade.html" title="class in be.ugent.intec.halvade">Halvade</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#makeRegionFile(org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.utils.ChromosomeRange,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20java.lang.String)">makeRegionFile(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, ChromosomeRange, PreprocessingTools, String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#makeRegionListFromFile(java.lang.String)">makeRegionListFromFile(String)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/AlignedBamMapper.html#map(org.apache.hadoop.io.LongWritable,%20org.seqdoop.hadoop_bam.SAMRecordWritable,%20org.apache.hadoop.mapreduce.Mapper.Context)">map(LongWritable, SAMRecordWritable, Mapper&lt;LongWritable, SAMRecordWritable, ChromosomeRegion, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/AlignedBamMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">AlignedBamMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/Bowtie2Mapper.html#map(org.apache.hadoop.io.LongWritable,%20org.apache.hadoop.io.Text,%20org.apache.hadoop.mapreduce.Mapper.Context)">map(LongWritable, Text, Mapper&lt;LongWritable, Text, ChromosomeRegion, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/Bowtie2Mapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">Bowtie2Mapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAAlnMapper.html#map(org.apache.hadoop.io.LongWritable,%20org.apache.hadoop.io.Text,%20org.apache.hadoop.mapreduce.Mapper.Context)">map(LongWritable, Text, Mapper&lt;LongWritable, Text, ChromosomeRegion, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAAlnMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BWAAlnMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAMemMapper.html#map(org.apache.hadoop.io.LongWritable,%20org.apache.hadoop.io.Text,%20org.apache.hadoop.mapreduce.Mapper.Context)">map(LongWritable, Text, Mapper&lt;LongWritable, Text, ChromosomeRegion, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAMemMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BWAMemMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/Cushaw2Mapper.html#map(org.apache.hadoop.io.LongWritable,%20org.apache.hadoop.io.Text,%20org.apache.hadoop.mapreduce.Mapper.Context)">map(LongWritable, Text, Mapper&lt;LongWritable, Text, ChromosomeRegion, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/Cushaw2Mapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">Cushaw2Mapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html#map(org.apache.hadoop.io.LongWritable,%20org.apache.hadoop.io.Text,%20org.apache.hadoop.mapreduce.Mapper.Context)">map(LongWritable, Text, Mapper&lt;LongWritable, Text, T1, T2&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineMapper.html#map(org.apache.hadoop.io.LongWritable,%20org.apache.hadoop.io.Text,%20org.apache.hadoop.mapreduce.Mapper.Context)">map(LongWritable, Text, Mapper.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HTSeqCombineMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html#map(org.apache.hadoop.io.LongWritable,%20org.apache.hadoop.io.Text,%20org.apache.hadoop.mapreduce.Mapper.Context)">map(LongWritable, Text, Mapper&lt;LongWritable, Text, GenomeSJ, Text&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">StarAlignPassXMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineMapper.html#map(org.apache.hadoop.io.LongWritable,%20org.seqdoop.hadoop_bam.VariantContextWritable,%20org.apache.hadoop.mapreduce.Mapper.Context)">map(LongWritable, VariantContextWritable, Mapper&lt;LongWritable, VariantContextWritable, LongWritable, VariantContextWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">VCFCombineMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#mapContainersPerNode">mapContainersPerNode</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/MapReduceRunner.html" title="class in be.ugent.intec.halvade"><span class="strong">MapReduceRunner</span></a> - Class in <a href="../be/ugent/intec/halvade/package-summary.html">be.ugent.intec.halvade</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/MapReduceRunner.html#MapReduceRunner()">MapReduceRunner()</a></span> - Constructor for class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/MapReduceRunner.html" title="class in be.ugent.intec.halvade">MapReduceRunner</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#maps">maps</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#maxQD">maxQD</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#mem">mem</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#mem">mem</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#MEM_ALN">MEM_ALN</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#MEM_AM">MEM_AM</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#MEM_ELPREP">MEM_ELPREP</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#MEM_REF">MEM_REF</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#MEM_STAR">MEM_STAR</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#mergeBam">mergeBam</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#mergeBam">mergeBam</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#mergeJS">mergeJS</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#MIN_GENE_SEPARATION">MIN_GENE_SEPARATION</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#MIN_THRESHOLD">MIN_THRESHOLD</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#minChrLength">minChrLength</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#minFS">minFS</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#mthreads">mthreads</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-</dl>
-<a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">K</a>&nbsp;<a href="index-12.html">L</a>&nbsp;<a href="index-13.html">M</a>&nbsp;<a href="index-14.html">N</a>&nbsp;<a href="index-15.html">O</a>&nbsp;<a href="index-16.html">P</a>&nbsp;<a href="index-17.html">Q</a>&nbsp;<a href="index-18.html">R</a>&nbsp;<a href="index-19.html">S</a>&nbsp;<a href="index-20.html">T</a>&nbsp;<a href="index-21.html">U</a>&nbsp;<a href="index-22.html">V</a>&nbsp;<a href="index-23.html">W</a>&nbsp;</div>
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-  if(window==top) {
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diff --git a/halvade/dist/javadoc/index-files/index-14.html b/halvade/dist/javadoc/index-files/index-14.html
deleted file mode 100644
index e712b65..0000000
--- a/halvade/dist/javadoc/index-files/index-14.html
+++ /dev/null
@@ -1,127 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
-<head>
-<!-- Generated by javadoc (version 1.7.0_91) on Sat Jan 23 21:38:55 CET 2016 -->
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<title>N-Index</title>
-<meta name="date" content="2016-01-23">
-<link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
-</head>
-<body>
-<script type="text/javascript"><!--
-    if (location.href.indexOf('is-external=true') == -1) {
-        parent.document.title="N-Index";
-    }
-//-->
-</script>
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-<div>JavaScript is disabled on your browser.</div>
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-<li>Package</li>
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-<li>Use</li>
-<li><a href="../overview-tree.html">Tree</a></li>
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-<li class="navBarCell1Rev">Index</li>
-<li><a href="../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
-<li><a href="index-13.html">Prev Letter</a></li>
-<li><a href="index-15.html">Next Letter</a></li>
-</ul>
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-<li><a href="index-14.html" target="_top">No Frames</a></li>
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-<div>
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-  if(window==top) {
-    allClassesLink.style.display = "block";
-  }
-  else {
-    allClassesLink.style.display = "none";
-  }
-  //-->
-</script>
-</div>
-<a name="skip-navbar_top">
-<!--   -->
-</a></div>
-<!-- ========= END OF TOP NAVBAR ========= -->
-<div class="contentContainer"><a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">K</a>&nbsp;<a href="index-12.html">L</a>&nbsp;<a href="index-13.html">M</a>&nbsp;<a href="index-14.html">N</a>&nbsp;<a href="index-15.html">O</a>&nbsp;<a href="index-16.html">P</a>&nbsp;<a href="index-17.html">Q</a>&nbsp;<a href="index-18.html">R</a>&nbsp;<a href="index-19.html">S</a>&nbsp;<a href="index-20.html">T</a>&nbsp;<a href="index-21.html">U</a>&nbsp;<a href="index-22.html">V</a>&nbsp;<a href="index-23.html">W</a>&nbsp;<a name="_N_">
-<!--   -->
-</a>
-<h2 class="title">N</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#newMaxQualScore">newMaxQualScore</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#next()">next()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#NO_CMD_HEADER">NO_CMD_HEADER</a></span> - Static variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#nodes">nodes</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-</dl>
-<a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">K</a>&nbsp;<a href="index-12.html">L</a>&nbsp;<a href="index-13.html">M</a>&nbsp;<a href="index-14.html">N</a>&nbsp;<a href="index-15.html">O</a>&nbsp;<a href="index-16.html">P</a>&nbsp;<a href="index-17.html">Q</a>&nbsp;<a href="index-18.html">R</a>&nbsp;<a href="index-19.html">S</a>&nbsp;<a href="index-20.html">T</a>&nbsp;<a href="index-21.html">U</a>&nbsp;<a href="index-22.html">V</a>&nbsp;<a href="index-23.html">W</a>&nbsp;</div>
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-<li>Class</li>
-<li>Use</li>
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-<li class="navBarCell1Rev">Index</li>
-<li><a href="../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
-<li><a href="index-13.html">Prev Letter</a></li>
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-</ul>
-<div>
-<script type="text/javascript"><!--
-  allClassesLink = document.getElementById("allclasses_navbar_bottom");
-  if(window==top) {
-    allClassesLink.style.display = "block";
-  }
-  else {
-    allClassesLink.style.display = "none";
-  }
-  //-->
-</script>
-</div>
-<a name="skip-navbar_bottom">
-<!--   -->
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-<!-- ======== END OF BOTTOM NAVBAR ======= -->
-</body>
-</html>
diff --git a/halvade/dist/javadoc/index-files/index-15.html b/halvade/dist/javadoc/index-files/index-15.html
deleted file mode 100644
index 9e13ed3..0000000
--- a/halvade/dist/javadoc/index-files/index-15.html
+++ /dev/null
@@ -1,143 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
-<head>
-<!-- Generated by javadoc (version 1.7.0_91) on Sat Jan 23 21:38:55 CET 2016 -->
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<title>O-Index</title>
-<meta name="date" content="2016-01-23">
-<link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
-</head>
-<body>
-<script type="text/javascript"><!--
-    if (location.href.indexOf('is-external=true') == -1) {
-        parent.document.title="O-Index";
-    }
-//-->
-</script>
-<noscript>
-<div>JavaScript is disabled on your browser.</div>
-</noscript>
-<!-- ========= START OF TOP NAVBAR ======= -->
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-<!--   -->
-</a><a href="#skip-navbar_top" title="Skip navigation links"></a><a name="navbar_top_firstrow">
-<!--   -->
-</a>
-<ul class="navList" title="Navigation">
-<li><a href="../overview-summary.html">Overview</a></li>
-<li>Package</li>
-<li>Class</li>
-<li>Use</li>
-<li><a href="../overview-tree.html">Tree</a></li>
-<li><a href="../deprecated-list.html">Deprecated</a></li>
-<li class="navBarCell1Rev">Index</li>
-<li><a href="../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
-<li><a href="index-14.html">Prev Letter</a></li>
-<li><a href="index-16.html">Next Letter</a></li>
-</ul>
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-<div>
-<script type="text/javascript"><!--
-  allClassesLink = document.getElementById("allclasses_navbar_top");
-  if(window==top) {
-    allClassesLink.style.display = "block";
-  }
-  else {
-    allClassesLink.style.display = "none";
-  }
-  //-->
-</script>
-</div>
-<a name="skip-navbar_top">
-<!--   -->
-</a></div>
-<!-- ========= END OF TOP NAVBAR ========= -->
-<div class="contentContainer"><a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">K</a>&nbsp;<a href="index-12.html">L</a>&nbsp;<a href="index-13.html">M</a>&nbsp;<a href="index-14.html">N</a>&nbsp;<a href="index-15.html">O</a>&nbsp;<a href="index-16.html">P</a>&nbsp;<a href="index-17.html">Q</a>&nbsp;<a href="index-18.html">R</a>&nbsp;<a href="index-19.html">S</a>&nbsp;<a href="index-20.html">T</a>&nbsp;<a href="index-21.html">U</a>&nbsp;<a href="index-22.html">V</a>&nbsp;<a href="index-23.html">W</a>&nbsp;<a name="_O_">
-<!--   -->
-</a>
-<h2 class="title">O</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#onedec">onedec</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#options">options</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#orderPartitionsBySize(java.lang.String)">orderPartitionsBySize(String)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#out">out</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#out">out</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#outHeader">outHeader</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#outKey">outKey</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#outpFormat">outpFormat</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#outputdir">outputdir</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#overhang">overhang</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#overrideMapMem">overrideMapMem</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#overrideRedMem">overrideRedMem</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-</dl>
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diff --git a/halvade/dist/javadoc/index-files/index-16.html b/halvade/dist/javadoc/index-files/index-16.html
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-<h2 class="title">P</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#paired">paired</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#parseArguments(java.lang.String[],%20org.apache.hadoop.conf.Configuration)">parseArguments(String[], Configuration)</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#parseDictFile(org.apache.hadoop.conf.Configuration)">parseDictFile(Configuration)</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html#parseSJString(java.lang.String,%20htsjdk.samtools.SAMSequenceDictionary)">parseSJString(String, SAMSequenceDictionary)</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">GenomeSJ</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#PASS1">PASS1</a></span> - Static variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html#PASS1_LOCK_VAL">PASS1_LOCK_VAL</a></span> - Static variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">StarAlignPassXMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#PASS2">PASS2</a></span> - Static variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html#PASS2_LOCK_VAL">PASS2_LOCK_VAL</a></span> - Static variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">StarAlignPassXMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#PicardPreprocess(org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.utils.SAMRecordIterator,%20java.lang.String)">PicardPreprocess(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, PreprocessingTools, SAMRecordIterator, String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html#position">position</a></span> - Variable in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools"><span class="strong">PreprocessingTools</span></a> - Class in <a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#PreprocessingTools(java.lang.String)">PreprocessingTools(String)</a></span> - Constructor for class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html#printDirectoryTree(java.io.File,%20int)">printDirectoryTree(File, int)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#printDirectoryTree(java.io.File,%20int)">printDirectoryTree(File, int)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#printDirectoryTree(java.io.File,%20int)">printDirectoryTree(File, int)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#privateDownloadFileFromHDFS(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20org.apache.hadoop.fs.FileSystem,%20java.lang.String,%20java.lang.String)">privateDownloadFileFromHDFS(TaskInputOutputContext, FileSystem, String, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#privateUploadFileToHDFS(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20org.apache.hadoop.fs.FileSystem,%20java.lang.String,%20java.lang.String)">privateUploadFileToHDFS(TaskInputOutputContext, FileSystem, String, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/DnaGATKReducer.html#processAlignments(java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.tools.GATKTools)">processAlignments(Iterable&lt;SAMRecordWritable&gt;, Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, PreprocessingTools, GATKTools)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/DnaGATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">DnaGATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#processAlignments(java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.tools.GATKTools)">processAlignments(Iterable&lt;SAMRecordWritable&gt;, Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, PreprocessingTools, GATKTools)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RnaGATKReducer.html#processAlignments(java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.tools.GATKTools)">processAlignments(Iterable&lt;SAMRecordWritable&gt;, Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, PreprocessingTools, GATKTools)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RnaGATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RnaGATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">ProcessBuilderWrapper</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#ProcessBuilderWrapper(java.lang.String[],%20java.lang.String)">ProcessBuilderWrapper(String[], String)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/tools/ProcessException.html" title="class in be.ugent.intec.halvade.tools"><span class="strong">ProcessException</span></a> - Exception in <a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/ProcessException.html#ProcessException(java.lang.String,%20int)">ProcessException(String, int)</a></span> - Constructor for exception be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/ProcessException.html" title="class in be.ugent.intec.halvade.tools">ProcessException</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/ProcessException.html#ProcessException(java.lang.String[],%20java.lang.String,%20int)">ProcessException(String[], String, int)</a></span> - Constructor for exception be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/ProcessException.html" title="class in be.ugent.intec.halvade.tools">ProcessException</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Logger.html#PROFILE(java.lang.String)">PROFILE(String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Logger.html" title="class in be.ugent.intec.halvade.utils">Logger</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#programNames">programNames</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
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diff --git a/halvade/dist/javadoc/index-files/index-17.html b/halvade/dist/javadoc/index-files/index-17.html
deleted file mode 100644
index 26bda0f..0000000
--- a/halvade/dist/javadoc/index-files/index-17.html
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-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/QualityEncoding.html#QualityEncoding()">QualityEncoding()</a></span> - Constructor for class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/QualityEncoding.html" title="class in be.ugent.intec.halvade.tools">QualityEncoding</a></dt>
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-<dt><a href="../be/ugent/intec/halvade/tools/QualityEncoding.QENCODING.html" title="enum in be.ugent.intec.halvade.tools"><span class="strong">QualityEncoding.QENCODING</span></a> - Enum in <a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></dt>
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-<dt><a href="../be/ugent/intec/halvade/tools/QualityException.html" title="class in be.ugent.intec.halvade.tools"><span class="strong">QualityException</span></a> - Exception in <a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></dt>
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diff --git a/halvade/dist/javadoc/index-files/index-18.html b/halvade/dist/javadoc/index-files/index-18.html
deleted file mode 100644
index dd681b4..0000000
--- a/halvade/dist/javadoc/index-files/index-18.html
+++ /dev/null
@@ -1,341 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-</a>
-<h2 class="title">R</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#r">r</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#read(java.nio.ByteBuffer)">read(ByteBuffer)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#read1File">read1File</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#read2File">read2File</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html#readcount">readcount</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#readCountsPerRegionFile">readCountsPerRegionFile</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html#readFields(java.io.DataInput)">readFields(DataInput)</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html#readFields(java.io.DataInput)">readFields(DataInput)</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">GenomeSJ</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html#reads">reads</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPair.html#reads">reads</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPair.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.KeyCountPair</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#reads">reads</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#rebuildStarGenome(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20int,%20int,%20long)">rebuildStarGenome(TaskInputOutputContext, String, String, String, String, int, int, long)</a></span> - Static method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">RebuildStarGenomeReducer</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#RebuildStarGenomeReducer()">RebuildStarGenomeReducer()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#recordWriter">recordWriter</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#redistribute">redistribute</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#redistribute">redistribute</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#redistribute">redistribute</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#reduce(be.ugent.intec.halvade.hadoop.datatypes.ChromosomeRegion,%20java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context)">reduce(ChromosomeRegion, Iterable&lt;SAMRecordWritable&gt;, Reducer&lt;ChromosomeRegion, SAMRecordWritable, LongWritable, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/CountReadsReducer.html#reduce(be.ugent.intec.halvade.hadoop.datatypes.ChromosomeRegion,%20java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context)">reduce(ChromosomeRegion, Iterable&lt;SAMRecordWritable&gt;, Reducer&lt;ChromosomeRegion, SAMRecordWritable, Text, LongWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/CountReadsReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">CountReadsReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#reduce(be.ugent.intec.halvade.hadoop.datatypes.ChromosomeRegion,%20java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context)">reduce(ChromosomeRegion, Iterable&lt;SAMRecordWritable&gt;, Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#reduce(be.ugent.intec.halvade.hadoop.datatypes.ChromosomeRegion,%20java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context)">reduce(ChromosomeRegion, Iterable&lt;SAMRecordWritable&gt;, Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineReducer.html#reduce(org.apache.hadoop.io.Text,%20java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context)">reduce(Text, Iterable&lt;LongWritable&gt;, Reducer&lt;Text, LongWritable, Text, LongWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HTSeqCombineReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#reduce(be.ugent.intec.halvade.hadoop.datatypes.GenomeSJ,%20java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context)">reduce(GenomeSJ, Iterable&lt;Text&gt;, Reducer&lt;GenomeSJ, Text, LongWritable, Text&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.html#reduce(org.apache.hadoop.io.LongWritable,%20java.lang.Iterable,%20org.apache.hadoop.mapreduce.Reducer.Context)">reduce(LongWritable, Iterable&lt;VariantContextWritable&gt;, Reducer&lt;LongWritable, VariantContextWritable, LongWritable, VariantContextWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">VCFCombineReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#REDUCE_TASKS_FACTOR">REDUCE_TASKS_FACTOR</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html#reduceNumber">reduceNumber</a></span> - Variable in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#reducerContainersPerNode">reducerContainersPerNode</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#reduces">reduces</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#ref">ref</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#ref">ref</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#ref">ref</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#ref">ref</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#REF_BOTH">REF_BOTH</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#REF_LOCK">REF_LOCK</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#refDir">refDir</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#referenceName">referenceName</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#regionCount">regionCount</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#regionLength">regionLength</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#regions">regions</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#regionsByChrom">regionsByChrom</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#releaseLock()">releaseLock()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#remove()">remove()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#removeAndReleaseLock()">removeAndReleaseLock()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#removeLocalDir(java.lang.String)">removeLocalDir(String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#removeLocalDir(boolean,%20java.lang.String)">removeLocalDir(boolean, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#removeLocalDir(java.lang.String,%20org.apache.hadoop.mapreduce.TaskInputOutputContext,%20be.ugent.intec.halvade.hadoop.mapreduce.HalvadeCounters)">removeLocalDir(String, TaskInputOutputContext, HalvadeCounters)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#removeLocalDir(boolean,%20java.lang.String,%20org.apache.hadoop.mapreduce.TaskInputOutputContext,%20be.ugent.intec.halvade.hadoop.mapreduce.HalvadeCounters)">removeLocalDir(boolean, String, TaskInputOutputContext, HalvadeCounters)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#removeLocalFile(java.lang.String)">removeLocalFile(String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#removeLocalFile(boolean,%20java.lang.String)">removeLocalFile(boolean, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#removeLocalFile(java.lang.String,%20org.apache.hadoop.mapreduce.TaskInputOutputContext,%20be.ugent.intec.halvade.hadoop.mapreduce.HalvadeCounters)">removeLocalFile(String, TaskInputOutputContext, HalvadeCounters)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#removeLocalFile(boolean,%20java.lang.String,%20org.apache.hadoop.mapreduce.TaskInputOutputContext,%20be.ugent.intec.halvade.hadoop.mapreduce.HalvadeCounters)">removeLocalFile(boolean, String, TaskInputOutputContext, HalvadeCounters)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#reorderRegions">reorderRegions</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#reportAll">reportAll</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#requireFixQuality">requireFixQuality</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#requireUploadToHDFS">requireUploadToHDFS</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#RESOURCE_REQ">RESOURCE_REQ</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#RETRIES">RETRIES</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#RGID">RGID</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#RGID">RGID</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#RGID">RGID</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#RGLB">RGLB</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#RGLB">RGLB</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#RGLB">RGLB</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#RGPL">RGPL</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#RGPL">RGPL</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#RGPL">RGPL</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#RGPU">RGPU</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#RGPU">RGPU</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#RGPU">RGPU</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#RGSM">RGSM</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#RGSM">RGSM</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#RGSM">RGSM</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/MapReduceRunner.html#RNA">RNA</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/MapReduceRunner.html" title="class in be.ugent.intec.halvade">MapReduceRunner</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/MapReduceRunner.html#RNA_PASS2">RNA_PASS2</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/MapReduceRunner.html" title="class in be.ugent.intec.halvade">MapReduceRunner</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#RNA_SHMEM_PASS1">RNA_SHMEM_PASS1</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#RNA_SHMEM_PASS2">RNA_SHMEM_PASS2</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RnaGATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">RnaGATKReducer</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RnaGATKReducer.html#RnaGATKReducer()">RnaGATKReducer()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RnaGATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RnaGATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#rnaPipeline">rnaPipeline</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#RnaVariantCalling(org.apache.hadoop.mapreduce.Reducer.Context,%20java.lang.String,%20be.ugent.intec.halvade.tools.GATKTools,%20java.lang.String,%20java.lang.String)">RnaVariantCalling(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, String, GATKTools, String, String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#roundOneDecimal(double)">roundOneDecimal(double)</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#roundOneDecimal(double)">roundOneDecimal(double)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#rthreads">rthreads</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.html#run(org.apache.hadoop.mapreduce.Reducer.Context)">run(Reducer&lt;LongWritable, VariantContextWritable, LongWritable, VariantContextWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">VCFCombineReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/MapReduceRunner.html#run(java.lang.String[])">run(String[])</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/MapReduceRunner.html" title="class in be.ugent.intec.halvade">MapReduceRunner</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMStreamHandler.html#run()">run()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMStreamHandler.html" title="class in be.ugent.intec.halvade.utils">SAMStreamHandler</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/StreamGobbler.html#run()">run()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/StreamGobbler.html" title="class in be.ugent.intec.halvade.utils">StreamGobbler</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#runAddOrReplaceReadGroups(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String)">runAddOrReplaceReadGroups(String, String, String, String, String, String, String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#runBaseRecalibrator(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String)">runBaseRecalibrator(String, String, String, String, String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#runBaseRecalibrator(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String[],%20java.lang.String)">runBaseRecalibrator(String, String, String, String[], String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#runBuildBamIndex(java.lang.String)">runBuildBamIndex(String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#runCleanSam(java.lang.String,%20java.lang.String)">runCleanSam(String, String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/MapReduceRunner.html#runCombineJob(java.lang.String,%20java.lang.String,%20boolean)">runCombineJob(String, String, boolean)</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/MapReduceRunner.html" title="class in be.ugent.intec.halvade">MapReduceRunner</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#runCombineVariants(java.lang.String[],%20java.lang.String,%20java.lang.String)">runCombineVariants(String[], String, String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#runFeatureCounts(java.lang.String,%20java.lang.String,%20java.lang.String,%20int)">runFeatureCounts(String, String, String, int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/MapReduceRunner.html#runHalvadeJob(org.apache.hadoop.conf.Configuration,%20java.lang.String,%20int)">runHalvadeJob(Configuration, String, int)</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/MapReduceRunner.html" title="class in be.ugent.intec.halvade">MapReduceRunner</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#runHaplotypeCaller(java.lang.String,%20java.lang.String,%20boolean,%20double,%20double,%20java.lang.String,%20java.lang.String[],%20java.lang.String)">runHaplotypeCaller(String, String, boolean, double, double, String, String[], String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#runIndelRealigner(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String)">runIndelRealigner(String, String, String, String, String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/Halvade.html#runMapReduce(java.lang.String[])">runMapReduce(String[])</a></span> - Static method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/Halvade.html" title="class in be.ugent.intec.halvade">Halvade</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#runMarkDuplicates(java.lang.String,%20java.lang.String,%20java.lang.String,%20boolean)">runMarkDuplicates(String, String, String, boolean)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/MapReduceRunner.html#runPass1RNAJob(org.apache.hadoop.conf.Configuration,%20java.lang.String)">runPass1RNAJob(Configuration, String)</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/MapReduceRunner.html" title="class in be.ugent.intec.halvade">MapReduceRunner</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html#runPass2">runPass2</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">StarAlignPassXMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#runPrintReads(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String)">runPrintReads(String, String, String, String, String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#runRealignerTargetCreator(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String)">runRealignerTargetCreator(String, String, String, String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#runSortVcf(java.lang.String,%20java.lang.String)">runSortVcf(String, String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#runSplitNCigarReads(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20int)">runSplitNCigarReads(String, String, String, String, int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/MapReduceRunner.html#runTimedJob(org.apache.hadoop.mapreduce.Job,%20java.lang.String)">runTimedJob(Job, String)</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/MapReduceRunner.html" title="class in be.ugent.intec.halvade">MapReduceRunner</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#runUnifiedGenotyper(java.lang.String,%20java.lang.String,%20double,%20double,%20java.lang.String,%20java.lang.String[],%20java.lang.String)">runUnifiedGenotyper(String, String, double, double, String, String[], String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#runVariantAnnotator(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String)">runVariantAnnotator(String, String, String, String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#runVariantFiltration(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20int,%20int,%20double,%20double)">runVariantFiltration(String, String, String, String, int, int, double, double)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
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diff --git a/halvade/dist/javadoc/index-files/index-19.html b/halvade/dist/javadoc/index-files/index-19.html
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@@ -1,386 +0,0 @@
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-</a>
-<h2 class="title">S</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#sam">sam</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">SAMRecordIterator</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#SAMRecordIterator(java.util.Iterator,%20htsjdk.samtools.SAMFileHeader)">SAMRecordIterator(Iterator&lt;SAMRecordWritable&gt;, SAMFileHeader)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#SAMRecordIterator(java.util.Iterator,%20htsjdk.samtools.SAMFileHeader,%20be.ugent.intec.halvade.utils.ChromosomeRange)">SAMRecordIterator(Iterator&lt;SAMRecordWritable&gt;, SAMFileHeader, ChromosomeRange)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/SAMStreamHandler.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">SAMStreamHandler</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMStreamHandler.html#SAMStreamHandler(be.ugent.intec.halvade.tools.AlignerInstance,%20org.apache.hadoop.mapreduce.Mapper.Context,%20boolean)">SAMStreamHandler(AlignerInstance, Mapper.Context, boolean)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMStreamHandler.html" title="class in be.ugent.intec.halvade.utils">SAMStreamHandler</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#SAMToolsMerge(java.lang.String,%20java.lang.String[],%20java.lang.String,%20int,%20java.lang.String)">SAMToolsMerge(String, String[], String, int, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#SAMToolsView(java.lang.String,%20java.lang.String,%20java.lang.String,%20int,%20boolean,%20java.lang.String)">SAMToolsView(String, String, String, int, boolean, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#samWritable">samWritable</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#scc">scc</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#sec">sec</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html#secondary_key">secondary_key</a></span> - Variable in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">GenomeSJ</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html#sequenceName">sequenceName</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange.Range</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setBed(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setBed(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setBedRegions(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setBedRegions(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setChrList(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setChrList(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html#setChromosomeRegion(int,%20int,%20int)">setChromosomeRegion(int, int, int)</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#setContext(org.apache.hadoop.mapreduce.Reducer.Context)">setContext(Reducer.Context)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#setContext(org.apache.hadoop.mapreduce.Reducer.Context)">setContext(Reducer.Context)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setCustomArgs(org.apache.hadoop.conf.Configuration,%20java.lang.String,%20java.lang.String,%20java.lang.String)">setCustomArgs(Configuration, String, String, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#setFileHeader(htsjdk.samtools.SAMFileHeader)">setFileHeader(SAMFileHeader)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setFilterBed(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setFilterBed(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setFilterDBSnp(org.apache.hadoop.conf.Configuration,%20boolean)">setFilterDBSnp(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setGff(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setGff(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/MapReduceRunner.html#setHeaderFile(java.lang.String,%20org.apache.hadoop.conf.Configuration)">setHeaderFile(String, Configuration)</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/MapReduceRunner.html" title="class in be.ugent.intec.halvade">MapReduceRunner</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setHeaderFile(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setHeaderFile(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setInputDir(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setInputDir(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setInputIsBam(org.apache.hadoop.conf.Configuration,%20boolean)">setInputIsBam(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setIsPaired(org.apache.hadoop.conf.Configuration,%20boolean)">setIsPaired(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setIsPass2(org.apache.hadoop.conf.Configuration,%20boolean)">setIsPass2(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setIsRNA(org.apache.hadoop.conf.Configuration,%20boolean)">setIsRNA(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#setJava(java.lang.String)">setJava(String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#setJava(java.lang.String)">setJava(String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setJava(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setJava(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#setJobResources(be.ugent.intec.halvade.HalvadeOptions,%20org.apache.hadoop.conf.Configuration,%20int,%20boolean,%20boolean)">setJobResources(HalvadeOptions, Configuration, int, boolean, boolean)</a></span> - Static method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setkeepChrSplitPairs(org.apache.hadoop.conf.Configuration,%20boolean)">setkeepChrSplitPairs(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setKeepDups(org.apache.hadoop.conf.Configuration,%20boolean)">setKeepDups(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setKeepFiles(org.apache.hadoop.conf.Configuration,%20boolean)">setKeepFiles(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setKnownSitesOnHDFS(org.apache.hadoop.conf.Configuration,%20java.lang.String[])">setKnownSitesOnHDFS(Configuration, String[])</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Logger.html#SETLEVEL(int)">SETLEVEL(int)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Logger.html" title="class in be.ugent.intec.halvade.utils">Logger</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setMapContainerCount(org.apache.hadoop.conf.Configuration,%20int)">setMapContainerCount(Configuration, int)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#setMapContainers">setMapContainers</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setMapThreads(org.apache.hadoop.conf.Configuration,%20int)">setMapThreads(Configuration, int)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setMergeBam(org.apache.hadoop.conf.Configuration,%20boolean)">setMergeBam(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setMinChrLength(org.apache.hadoop.conf.Configuration,%20int)">setMinChrLength(Configuration, int)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setOutDir(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setOutDir(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html#setOverhang(int)">setOverhang(int)</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">GenomeSJ</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setReadGroup(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setReadGroup(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setRedistribute(org.apache.hadoop.conf.Configuration,%20boolean)">setRedistribute(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#setReduceContainers">setReduceContainers</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setReducerThreads(org.apache.hadoop.conf.Configuration,%20int)">setReducerThreads(Configuration, int)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setRefDirOnScratch(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setRefDirOnScratch(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setRefOnHDFS(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setRefOnHDFS(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setRefSize(org.apache.hadoop.conf.Configuration,%20long)">setRefSize(Configuration, long)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html#setRegion(int,%20int)">setRegion(int, int)</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">GenomeSJ</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setReportAllVariant(org.apache.hadoop.conf.Configuration,%20boolean)">setReportAllVariant(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setSCC(org.apache.hadoop.conf.Configuration,%20double)">setSCC(Configuration, double)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setScratchTempDir(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setScratchTempDir(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setSEC(org.apache.hadoop.conf.Configuration,%20double)">setSEC(Configuration, double)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setSequenceDictionary(org.apache.hadoop.conf.Configuration,%20htsjdk.samtools.SAMSequenceDictionary)">setSequenceDictionary(Configuration, SAMSequenceDictionary)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setStarDirOnHDFS(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setStarDirOnHDFS(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setStarDirPass2HDFS(org.apache.hadoop.conf.Configuration,%20java.lang.String)">setStarDirPass2HDFS(Configuration, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#setThreadingType(int)">setThreadingType(int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#setThreads(int)">setThreads(int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#setThreads(int)">setThreads(int)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/AlignedBamMapper.html#setup(org.apache.hadoop.mapreduce.Mapper.Context)">setup(Mapper&lt;LongWritable, SAMRecordWritable, ChromosomeRegion, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/AlignedBamMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">AlignedBamMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#setup(org.apache.hadoop.mapreduce.Reducer.Context)">setup(Reducer&lt;ChromosomeRegion, SAMRecordWritable, LongWritable, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/Bowtie2Mapper.html#setup(org.apache.hadoop.mapreduce.Mapper.Context)">setup(Mapper&lt;LongWritable, Text, ChromosomeRegion, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/Bowtie2Mapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">Bowtie2Mapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAAlnMapper.html#setup(org.apache.hadoop.mapreduce.Mapper.Context)">setup(Mapper&lt;LongWritable, Text, ChromosomeRegion, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAAlnMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BWAAlnMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAMemMapper.html#setup(org.apache.hadoop.mapreduce.Mapper.Context)">setup(Mapper&lt;LongWritable, Text, ChromosomeRegion, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAMemMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BWAMemMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/Cushaw2Mapper.html#setup(org.apache.hadoop.mapreduce.Mapper.Context)">setup(Mapper&lt;LongWritable, Text, ChromosomeRegion, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/Cushaw2Mapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">Cushaw2Mapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#setup(org.apache.hadoop.mapreduce.Reducer.Context)">setup(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html#setup(org.apache.hadoop.mapreduce.Mapper.Context)">setup(Mapper&lt;LongWritable, Text, T1, T2&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#setup(org.apache.hadoop.mapreduce.Reducer.Context)">setup(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#setup(org.apache.hadoop.mapreduce.Reducer.Context)">setup(Reducer&lt;GenomeSJ, Text, LongWritable, Text&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html#setup(org.apache.hadoop.mapreduce.Mapper.Context)">setup(Mapper&lt;LongWritable, Text, GenomeSJ, Text&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">StarAlignPassXMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.html#setup(org.apache.hadoop.mapreduce.Reducer.Context)">setup(Reducer&lt;LongWritable, VariantContextWritable, LongWritable, VariantContextWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">VCFCombineReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setUpdateReadGroup(org.apache.hadoop.conf.Configuration,%20boolean)">setUpdateReadGroup(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setUseElPrep(org.apache.hadoop.conf.Configuration,%20boolean)">setUseElPrep(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setUseUnifiedGenotyper(org.apache.hadoop.conf.Configuration,%20boolean)">setUseUnifiedGenotyper(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#setVcores(org.apache.hadoop.conf.Configuration,%20int)">setVcores(Configuration, int)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html#SH_MEM_LOCK">SH_MEM_LOCK</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">StarAlignPassXMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/partitioners/SimpleChrRegionComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners"><span class="strong">SimpleChrRegionComparator</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/partitioners/package-summary.html">be.ugent.intec.halvade.hadoop.partitioners</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/partitioners/SimpleChrRegionComparator.html#SimpleChrRegionComparator()">SimpleChrRegionComparator()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.partitioners.<a href="../be/ugent/intec/halvade/hadoop/partitioners/SimpleChrRegionComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners">SimpleChrRegionComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#sites">sites</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html#sj">sj</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">StarAlignPassXMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#sj">sj</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#smtEnabled">smtEnabled</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#snpSift(java.util.ArrayList,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20int)">snpSift(ArrayList&lt;String&gt;, String, String, String, String, int)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#sparseGenome">sparseGenome</a></span> - Static variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>
-<div class="block"><avoid rebuilding genome>
- first pass:
- ./STAR 
-  --runThreadN 2 
-  --genomeDir ./genTest/ 
-  --genomeLoad LoadAndKeep 
-  --readFilesIn ../reads1_m_000001_0.fastq ../reads2_m_000001_0.fastq 
- 
- second pass:
- ./STAR 
-  --runThreadN 2 
-  --genomeDir ./genTest/ 
-  --genomeLoad LoadAndKeep 
-  --readFilesIn ../reads1_m_000001_0.fastq ../reads2_m_000001_0.fastq 
-  --twopassMode Basic 
-  --sjdbFileChrStartEnd FileName.sjdb
- 
- but cant be used with shared memory yet!</div>
-</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#splitNTrim(org.apache.hadoop.mapreduce.Reducer.Context,%20java.lang.String,%20be.ugent.intec.halvade.tools.GATKTools,%20java.lang.String,%20java.lang.String)">splitNTrim(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, String, GATKTools, String, String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#splitter">splitter</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#stand_call_conf">stand_call_conf</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#stand_emit_conf">stand_emit_conf</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#STAR_REF_FILES">STAR_REF_FILES</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#STAR_REF_OPTIONAL_FILES">STAR_REF_OPTIONAL_FILES</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html#star_shmem_lock">star_shmem_lock</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">StarAlignPassXMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#starAlign(java.lang.String,%20int,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20int,%20int,%20int,%20java.lang.String)">starAlign(String, int, String, String, String, String, int, int, int, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">StarAlignPassXMapper</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html#StarAlignPassXMapper()">StarAlignPassXMapper()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">StarAlignPassXMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#STARG_LOCK">STARG_LOCK</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#STARGenome">STARGenome</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#starGenomeLoad(java.lang.String,%20java.lang.String,%20boolean)">starGenomeLoad(String, String, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools"><span class="strong">STARInstance</span></a> - Class in <a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#starRebuildGenome(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20int,%20int,%20long,%20boolean)">starRebuildGenome(String, String, String, String, int, int, long, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html#start">start</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Timer.html#start()">start()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Timer.html" title="class in be.ugent.intec.halvade.utils">Timer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#startAligner(org.apache.hadoop.mapreduce.Mapper.Context)">startAligner(Mapper.Context)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html#startAligner(org.apache.hadoop.mapreduce.Mapper.Context)">startAligner(Mapper.Context)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html" title="class in be.ugent.intec.halvade.tools">Bowtie2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html#startAligner(org.apache.hadoop.mapreduce.Mapper.Context)">startAligner(Mapper.Context)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">BWAAlnInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html#startAligner(org.apache.hadoop.mapreduce.Mapper.Context)">startAligner(Mapper.Context)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html" title="class in be.ugent.intec.halvade.tools">BWAMemInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html#startAligner(org.apache.hadoop.mapreduce.Mapper.Context)">startAligner(Mapper.Context)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html" title="class in be.ugent.intec.halvade.tools">Cushaw2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html#startAligner(org.apache.hadoop.mapreduce.Mapper.Context)">startAligner(Mapper.Context)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html" title="class in be.ugent.intec.halvade.tools">DummyAlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#startAligner(org.apache.hadoop.mapreduce.Mapper.Context)">startAligner(Mapper.Context)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#startProcess()">startProcess()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#startProcess(boolean)">startProcess(boolean)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#startProcess(java.io.PrintStream,%20java.io.PrintStream)">startProcess(PrintStream, PrintStream)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#startupJob">startupJob</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Timer.html#stop()">stop()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Timer.html" title="class in be.ugent.intec.halvade.utils">Timer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#streamElPrep(org.apache.hadoop.mapreduce.Reducer.Context,%20java.lang.String,%20java.lang.String,%20int,%20be.ugent.intec.halvade.utils.SAMRecordIterator,%20htsjdk.samtools.SAMFileHeader,%20java.lang.String,%20boolean,%20java.lang.String)">streamElPrep(Reducer.Context, String, String, int, SAMRecordIterator, SAMFileHeader, String, boolean, String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/StreamGobbler.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">StreamGobbler</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/StreamGobbler.html#StreamGobbler(java.io.InputStream,%20java.io.PrintStream)">StreamGobbler(InputStream, PrintStream)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/StreamGobbler.html" title="class in be.ugent.intec.halvade.utils">StreamGobbler</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/StreamGobbler.html#StreamGobbler(java.io.InputStream,%20java.io.PrintStream,%20java.lang.String)">StreamGobbler(InputStream, PrintStream, String)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/StreamGobbler.html" title="class in be.ugent.intec.halvade.utils">StreamGobbler</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#stub">stub</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-</dl>
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diff --git a/halvade/dist/javadoc/index-files/index-2.html b/halvade/dist/javadoc/index-files/index-2.html
deleted file mode 100644
index 5b0b757..0000000
--- a/halvade/dist/javadoc/index-files/index-2.html
+++ /dev/null
@@ -1,187 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
-<head>
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-<title>B-Index</title>
-<meta name="date" content="2016-01-23">
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-<!--   -->
-</a>
-<h2 class="title">B</h2>
-<dl>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">BamMergeReducer</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#BamMergeReducer()">BamMergeReducer()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#bamrg">bamrg</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#bamrg">bamrg</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#baseQualityScoreRecalibration(org.apache.hadoop.mapreduce.Reducer.Context,%20java.lang.String,%20be.ugent.intec.halvade.utils.ChromosomeRange,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.tools.GATKTools,%20java.lang.String,%20java.lang.String)">baseQualityScoreRecalibration(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, String, ChromosomeRange, PreprocessingTools, GATKTools, String, String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/package-summary.html">be.ugent.intec.halvade</a> - package be.ugent.intec.halvade</dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/datatypes/package-summary.html">be.ugent.intec.halvade.hadoop.datatypes</a> - package be.ugent.intec.halvade.hadoop.datatypes</dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a> - package be.ugent.intec.halvade.hadoop.mapreduce</dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/partitioners/package-summary.html">be.ugent.intec.halvade.hadoop.partitioners</a> - package be.ugent.intec.halvade.hadoop.partitioners</dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a> - package be.ugent.intec.halvade.tools</dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a> - package be.ugent.intec.halvade.utils</dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#bedFile">bedFile</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#bedRegion">bedRegion</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#bedTools(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String)">bedTools(String, String, String, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#bin">bin</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#bin">bin</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#bin">bin</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#bin">bin</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#bowtie2(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20int,%20java.lang.String)">bowtie2(String, String, String, String, int, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#BOWTIE2_REF_FILES">BOWTIE2_REF_FILES</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html" title="class in be.ugent.intec.halvade.tools"><span class="strong">Bowtie2Instance</span></a> - Class in <a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/Bowtie2Mapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">Bowtie2Mapper</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/Bowtie2Mapper.html#Bowtie2Mapper()">Bowtie2Mapper()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/Bowtie2Mapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">Bowtie2Mapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#bw">bw</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#BWA_REF_FILES">BWA_REF_FILES</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#bwaAln(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20int,%20java.lang.String)">bwaAln(String, String, String, String, int, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools"><span class="strong">BWAAlnInstance</span></a> - Class in <a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAAlnMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">BWAAlnMapper</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAAlnMapper.html#BWAAlnMapper()">BWAAlnMapper()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAAlnMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BWAAlnMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#bwaMem(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20boolean,%20boolean,%20int,%20java.lang.String)">bwaMem(String, String, String, String, boolean, boolean, int, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html" title="class in be.ugent.intec.halvade.tools"><span class="strong">BWAMemInstance</span></a> - Class in <a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAMemMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">BWAMemMapper</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAMemMapper.html#BWAMemMapper()">BWAMemMapper()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BWAMemMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BWAMemMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#bwaSamXe(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20boolean,%20int,%20java.lang.String)">bwaSamXe(String, String, String, String, String, String, boolean, int, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-</dl>
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-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#taskId">taskId</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#taskId">taskId</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#taskNr">taskNr</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#tasksLeft">tasksLeft</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
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-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#threads">threads</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#threads">threads</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#threads">threads</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/Timer.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">Timer</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Timer.html#Timer()">Timer()</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Timer.html" title="class in be.ugent.intec.halvade.utils">Timer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#tmp">tmp</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#tmpDir">tmpDir</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html#tmpDir">tmpDir</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">StarAlignPassXMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#tmpDir">tmpDir</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#tmpdir">tmpdir</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
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-<dd>&nbsp;</dd>
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-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html#toString()">toString()</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html#toString()">toString()</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">GenomeSJ</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/ProcessException.html#toString()">toString()</a></span> - Method in exception be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/ProcessException.html" title="class in be.ugent.intec.halvade.tools">ProcessException</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/QualityException.html#toString()">toString()</a></span> - Method in exception be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/QualityException.html" title="class in be.ugent.intec.halvade.tools">QualityException</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html#toString()">toString()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html#toString()">toString()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPair.html#toString()">toString()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPair.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.KeyCountPair</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Timer.html#toString()">toString()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Timer.html" title="class in be.ugent.intec.halvade.utils">Timer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#totalKeyCount">totalKeyCount</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#totalValCount">totalValCount</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html#type">type</a></span> - Variable in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">GenomeSJ</a></dt>
-<dd>&nbsp;</dd>
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-<h2 class="title">U</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#Unzip(java.lang.String)">Unzip(String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#updateRG">updateRG</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#updateRG">updateRG</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#uploadFileToHDFS(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20org.apache.hadoop.fs.FileSystem,%20java.lang.String,%20java.lang.String)">uploadFileToHDFS(TaskInputOutputContext, FileSystem, String, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#useBamInput">useBamInput</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMStreamHandler.html#useCompact">useCompact</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMStreamHandler.html" title="class in be.ugent.intec.halvade.utils">SAMStreamHandler</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#useElPrep">useElPrep</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#useGenotyper">useGenotyper</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#useUnifiedGenotyper">useUnifiedGenotyper</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
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diff --git a/halvade/dist/javadoc/index-files/index-22.html b/halvade/dist/javadoc/index-files/index-22.html
deleted file mode 100644
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--- a/halvade/dist/javadoc/index-files/index-22.html
+++ /dev/null
@@ -1,153 +0,0 @@
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-</a>
-<h2 class="title">V</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#val">val</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeCounters.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeCounters.html" title="enum in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeCounters</a></dt>
-<dd>
-<div class="block">Returns the enum constant of this type with the specified name.</div>
-</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/QualityEncoding.QENCODING.html#valueOf(java.lang.String)">valueOf(String)</a></span> - Static method in enum be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/QualityEncoding.QENCODING.html" title="enum in be.ugent.intec.halvade.tools">QualityEncoding.QENCODING</a></dt>
-<dd>
-<div class="block">Returns the enum constant of this type with the specified name.</div>
-</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeCounters.html#values()">values()</a></span> - Static method in enum be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeCounters.html" title="enum in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeCounters</a></dt>
-<dd>
-<div class="block">Returns an array containing the constants of this enum type, in
-the order they are declared.</div>
-</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/QualityEncoding.QENCODING.html#values()">values()</a></span> - Static method in enum be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/QualityEncoding.QENCODING.html" title="enum in be.ugent.intec.halvade.tools">QualityEncoding.QENCODING</a></dt>
-<dd>
-<div class="block">Returns an array containing the constants of this enum type, in
-the order they are declared.</div>
-</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#variantFiles">variantFiles</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">VCFCombineMapper</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineMapper.html#VCFCombineMapper()">VCFCombineMapper()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">VCFCombineMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">VCFCombineReducer</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.html#VCFCombineReducer()">VCFCombineReducer()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">VCFCombineReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#vcores">vcores</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#VCORES_AM">VCORES_AM</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-</dl>
-<a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">K</a>&nbsp;<a href="index-12.html">L</a>&nbsp;<a href="index-13.html">M</a>&nbsp;<a href="index-14.html">N</a>&nbsp;<a href="index-15.html">O</a>&nbsp;<a href="index-16.html">P</a>&nbsp;<a href="index-17.html">Q</a>&nbsp;<a href="index-18.html">R</a>&nbsp;<a href="index-19.html">S</a>&nbsp;<a href="index-20.html">T</a>&nbsp;<a href="index-21.html">U</a>&nbsp;<a href="index-22.html">V</a>&nbsp;<a href="index-23.html">W</a>&nbsp;</div>
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diff --git a/halvade/dist/javadoc/index-files/index-23.html b/halvade/dist/javadoc/index-files/index-23.html
deleted file mode 100644
index 41aadf5..0000000
--- a/halvade/dist/javadoc/index-files/index-23.html
+++ /dev/null
@@ -1,143 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#waitForCompletion()">waitForCompletion()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#windows">windows</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#writableRecord">writableRecord</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#writableRegion">writableRegion</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html#write(java.io.DataOutput)">write(DataOutput)</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html#write(java.io.DataOutput)">write(DataOutput)</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">GenomeSJ</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#writeableCompactRegion">writeableCompactRegion</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#writePairedSAMRecordToContext(htsjdk.samtools.SAMRecord,%20boolean)">writePairedSAMRecordToContext(SAMRecord, boolean)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#writeSAMRecordToContext(htsjdk.samtools.SAMRecord,%20boolean)">writeSAMRecordToContext(SAMRecord, boolean)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html#writeToBedRegionFile(java.lang.String,%20int)">writeToBedRegionFile(String, int)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html#writeToBedRegionFile(java.lang.String)">writeToBedRegionFile(String)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html#writeToPicardRegionFile(java.lang.String)">writeToPicardRegionFile(String)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange</a></dt>
-<dd>&nbsp;</dd>
-</dl>
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diff --git a/halvade/dist/javadoc/index-files/index-3.html b/halvade/dist/javadoc/index-files/index-3.html
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+++ /dev/null
@@ -1,291 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<!--   -->
-</a>
-<h2 class="title">C</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#callElPrep(java.lang.String,%20java.lang.String,%20java.lang.String,%20int,%20be.ugent.intec.halvade.utils.SAMRecordIterator,%20htsjdk.samtools.SAMFileHeader,%20java.lang.String,%20boolean,%20java.lang.String)">callElPrep(String, String, String, int, SAMRecordIterator, SAMFileHeader, String, boolean, String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#callSAMToBAM(java.lang.String,%20java.lang.String,%20int,%20boolean)">callSAMToBAM(String, String, int, boolean)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html#checkBinaries(org.apache.hadoop.mapreduce.Mapper.Context)">checkBinaries(Mapper&lt;LongWritable, Text, T1, T2&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#checkBinaries(org.apache.hadoop.mapreduce.Reducer.Context)">checkBinaries(Reducer.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#checkBinaries(org.apache.hadoop.mapreduce.Reducer.Context)">checkBinaries(Reducer.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#checkCorrectSize(java.lang.String,%20java.lang.String,%20org.apache.hadoop.fs.FileSystem)">checkCorrectSize(String, String, FileSystem)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#checkVcfIsNotEmpty(java.lang.String)">checkVcfIsNotEmpty(String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#chr">chr</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#chr">chr</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html#chromosome">chromosome</a></span> - Variable in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">ChromosomeRange</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html#ChromosomeRange()">ChromosomeRange()</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">ChromosomeRange.Range</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html#ChromosomeRange.Range(java.lang.String,%20int,%20int)">ChromosomeRange.Range(String, int, int)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange.Range</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes"><span class="strong">ChromosomeRegion</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/datatypes/package-summary.html">be.ugent.intec.halvade.hadoop.datatypes</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html#ChromosomeRegion()">ChromosomeRegion()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">ChromosomeSplitter</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#ChromosomeSplitter(htsjdk.samtools.SAMSequenceDictionary,%20java.lang.String,%20int)">ChromosomeSplitter(SAMSequenceDictionary, String, int)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#ChromosomeSplitter(htsjdk.samtools.SAMSequenceDictionary,%20int)">ChromosomeSplitter(SAMSequenceDictionary, int)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#ChromosomeSplitter(htsjdk.samtools.SAMSequenceDictionary,%20java.lang.String,%20int,%20boolean)">ChromosomeSplitter(SAMSequenceDictionary, String, int, boolean)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#ChromosomeSplitter(java.lang.String,%20org.apache.hadoop.conf.Configuration)">ChromosomeSplitter(String, Configuration)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">ChromosomeSplitter.BedRegion</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegionComparator.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">ChromosomeSplitter.BedRegionComparator</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegionComparator.html#ChromosomeSplitter.BedRegionComparator()">ChromosomeSplitter.BedRegionComparator()</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegionComparator.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegionComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPair.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">ChromosomeSplitter.KeyCountPair</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPair.html#ChromosomeSplitter.KeyCountPair(int,%20int)">ChromosomeSplitter.KeyCountPair(int, int)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPair.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.KeyCountPair</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPairComparator.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">ChromosomeSplitter.KeyCountPairComparator</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPairComparator.html#ChromosomeSplitter.KeyCountPairComparator()">ChromosomeSplitter.KeyCountPairComparator()</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPairComparator.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.KeyCountPairComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgGroupingComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners"><span class="strong">ChrRgGroupingComparator</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/partitioners/package-summary.html">be.ugent.intec.halvade.hadoop.partitioners</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgGroupingComparator.html#ChrRgGroupingComparator()">ChrRgGroupingComparator()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.partitioners.<a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgGroupingComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners">ChrRgGroupingComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgPartitioner.html" title="class in be.ugent.intec.halvade.hadoop.partitioners"><span class="strong">ChrRgPartitioner</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/partitioners/package-summary.html">be.ugent.intec.halvade.hadoop.partitioners</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgPartitioner.html#ChrRgPartitioner()">ChrRgPartitioner()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.partitioners.<a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgPartitioner.html" title="class in be.ugent.intec.halvade.hadoop.partitioners">ChrRgPartitioner</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgSortComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners"><span class="strong">ChrRgSortComparator</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/partitioners/package-summary.html">be.ugent.intec.halvade.hadoop.partitioners</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgSortComparator.html#ChrRgSortComparator()">ChrRgSortComparator()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.partitioners.<a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgSortComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners">ChrRgSortComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#chrString">chrString</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#cleanup(org.apache.hadoop.mapreduce.Reducer.Context)">cleanup(Reducer&lt;ChromosomeRegion, SAMRecordWritable, LongWritable, SAMRecordWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html#cleanup(org.apache.hadoop.mapreduce.Mapper.Context)">cleanup(Mapper&lt;LongWritable, Text, T1, T2&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#cleanup(org.apache.hadoop.mapreduce.Reducer.Context)">cleanup(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#cleanup(org.apache.hadoop.mapreduce.Reducer.Context)">cleanup(Reducer&lt;GenomeSJ, Text, LongWritable, Text&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html#cleanup(org.apache.hadoop.mapreduce.Mapper.Context)">cleanup(Mapper&lt;LongWritable, Text, GenomeSJ, Text&gt;.Context)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">StarAlignPassXMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#clearTaskFiles(org.apache.hadoop.conf.Configuration)">clearTaskFiles(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#closeAligner()">closeAligner()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html#closeAligner()">closeAligner()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html" title="class in be.ugent.intec.halvade.tools">Bowtie2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html#closeAligner()">closeAligner()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">BWAAlnInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html#closeAligner()">closeAligner()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html" title="class in be.ugent.intec.halvade.tools">BWAMemInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html#closeAligner()">closeAligner()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html" title="class in be.ugent.intec.halvade.tools">Cushaw2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html#closeAligner()">closeAligner()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html" title="class in be.ugent.intec.halvade.tools">DummyAlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#closeAligner()">closeAligner()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#cluster">cluster</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#COMBINE">COMBINE</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#combineVcf">combineVcf</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">CommandGenerator</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#CommandGenerator()">CommandGenerator()</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgGroupingComparator.html#compare(org.apache.hadoop.io.WritableComparable,%20org.apache.hadoop.io.WritableComparable)">compare(WritableComparable, WritableComparable)</a></span> - Method in class be.ugent.intec.halvade.hadoop.partitioners.<a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgGroupingComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners">ChrRgGroupingComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgSortComparator.html#compare(org.apache.hadoop.io.WritableComparable,%20org.apache.hadoop.io.WritableComparable)">compare(WritableComparable, WritableComparable)</a></span> - Method in class be.ugent.intec.halvade.hadoop.partitioners.<a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgSortComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners">ChrRgSortComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/partitioners/GenomeSJGroupingComparator.html#compare(org.apache.hadoop.io.WritableComparable,%20org.apache.hadoop.io.WritableComparable)">compare(WritableComparable, WritableComparable)</a></span> - Method in class be.ugent.intec.halvade.hadoop.partitioners.<a href="../be/ugent/intec/halvade/hadoop/partitioners/GenomeSJGroupingComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners">GenomeSJGroupingComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/partitioners/GenomeSJSortComparator.html#compare(org.apache.hadoop.io.WritableComparable,%20org.apache.hadoop.io.WritableComparable)">compare(WritableComparable, WritableComparable)</a></span> - Method in class be.ugent.intec.halvade.hadoop.partitioners.<a href="../be/ugent/intec/halvade/hadoop/partitioners/GenomeSJSortComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners">GenomeSJSortComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/partitioners/SimpleChrRegionComparator.html#compare(org.apache.hadoop.io.WritableComparable,%20org.apache.hadoop.io.WritableComparable)">compare(WritableComparable, WritableComparable)</a></span> - Method in class be.ugent.intec.halvade.hadoop.partitioners.<a href="../be/ugent/intec/halvade/hadoop/partitioners/SimpleChrRegionComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners">SimpleChrRegionComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegionComparator.html#compare(be.ugent.intec.halvade.utils.ChromosomeSplitter.BedRegion,%20be.ugent.intec.halvade.utils.ChromosomeSplitter.BedRegion)">compare(ChromosomeSplitter.BedRegion, ChromosomeSplitter.BedRegion)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegionComparator.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegionComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPairComparator.html#compare(be.ugent.intec.halvade.utils.ChromosomeSplitter.KeyCountPair,%20be.ugent.intec.halvade.utils.ChromosomeSplitter.KeyCountPair)">compare(ChromosomeSplitter.KeyCountPair, ChromosomeSplitter.KeyCountPair)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.KeyCountPairComparator.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.KeyCountPairComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html#compareTo(be.ugent.intec.halvade.hadoop.datatypes.ChromosomeRegion)">compareTo(ChromosomeRegion)</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html#compareTo(be.ugent.intec.halvade.hadoop.datatypes.GenomeSJ)">compareTo(GenomeSJ)</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">GenomeSJ</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#containers">containers</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#containers">containers</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#context">context</a></span> - Static variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#context">context</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html#contig">contig</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html#count">count</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#count">count</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html#count">count</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">RebuildStarGenomeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#countOnly">countOnly</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/CountReadsReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">CountReadsReducer</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/CountReadsReducer.html#CountReadsReducer()">CountReadsReducer()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/CountReadsReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">CountReadsReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#coverage">coverage</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#createOptions()">createOptions()</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#createReadGroupRecord(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String)">createReadGroupRecord(String, String, String, String, String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#createReadGroupRecord(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20htsjdk.samtools.util.Iso8601Date,%20java.lang.Integer)">createReadGroupRecord(String, String, String, String, String, String, String, Iso8601Date, Integer)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#createReadGroupRecordString(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String)">createReadGroupRecordString(String, String, String, String, String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#currentChr">currentChr</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#currentEnd">currentEnd</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#currentStart">currentStart</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#cushaw2(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20int,%20java.lang.String)">cushaw2(String, String, String, String, int, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#CUSHAW2_REF_FILES">CUSHAW2_REF_FILES</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html" title="class in be.ugent.intec.halvade.tools"><span class="strong">Cushaw2Instance</span></a> - Class in <a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/Cushaw2Mapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">Cushaw2Mapper</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/Cushaw2Mapper.html#Cushaw2Mapper()">Cushaw2Mapper()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/Cushaw2Mapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">Cushaw2Mapper</a></dt>
-<dd>&nbsp;</dd>
-</dl>
-<a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">K</a>&nbsp;<a href="index-12.html">L</a>&nbsp;<a href="index-13.html">M</a>&nbsp;<a href="index-14.html">N</a>&nbsp;<a href="index-15.html">O</a>&nbsp;<a href="index-16.html">P</a>&nbsp;<a href="index-17.html">Q</a>&nbsp;<a href="index-18.html">R</a>&nbsp;<a href="index-19.html">S</a>&nbsp;<a href="index-20.html">T</a>&nbsp;<a href="index-21.html">U</a>&nbsp;<a href="index-22.html">V</a>&nbsp;<a href="index-23.html">W</a>&nbsp;</div>
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diff --git a/halvade/dist/javadoc/index-files/index-4.html b/halvade/dist/javadoc/index-files/index-4.html
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--- a/halvade/dist/javadoc/index-files/index-4.html
+++ /dev/null
@@ -1,179 +0,0 @@
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-<!--   -->
-</a>
-<h2 class="title">D</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#DBSNP_LOCK">DBSNP_LOCK</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Logger.html#DEBUG(java.lang.String)">DEBUG(String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Logger.html" title="class in be.ugent.intec.halvade.utils">Logger</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Logger.html#DEBUG(java.lang.String,%20int)">DEBUG(String, int)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Logger.html" title="class in be.ugent.intec.halvade.utils">Logger</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#DEFAULT_COVERAGE">DEFAULT_COVERAGE</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#DEFAULT_COVERAGE_SIZE">DEFAULT_COVERAGE_SIZE</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#DEFAULT_LOCK_VAL">DEFAULT_LOCK_VAL</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#deleteDir(java.io.File)">deleteDir(File)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#dict">dict</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#dict">dict</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#dict">dict</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#dict">dict</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#DICT_SUFFIX">DICT_SUFFIX</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#dir">dir</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#DISABLE_VCF_LOCKING">DISABLE_VCF_LOCKING</a></span> - Static variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#DNA">DNA</a></span> - Static variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/MapReduceRunner.html#DNA">DNA</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/MapReduceRunner.html" title="class in be.ugent.intec.halvade">MapReduceRunner</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/DnaGATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">DnaGATKReducer</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/DnaGATKReducer.html#DnaGATKReducer()">DnaGATKReducer()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/DnaGATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">DnaGATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#DnaVariantCalling(org.apache.hadoop.mapreduce.Reducer.Context,%20java.lang.String,%20be.ugent.intec.halvade.tools.GATKTools,%20java.lang.String,%20java.lang.String)">DnaVariantCalling(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, String, GATKTools, String, String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#downloadAlignerIndex(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String[])">downloadAlignerIndex(TaskInputOutputContext, String, String, String, String[])</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#downloadBowtie2Index(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20java.lang.String)">downloadBowtie2Index(TaskInputOutputContext, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#downloadBWAIndex(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20java.lang.String)">downloadBWAIndex(TaskInputOutputContext, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#downloadCushaw2Index(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20java.lang.String)">downloadCushaw2Index(TaskInputOutputContext, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#downloadFileFromHDFS(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20org.apache.hadoop.fs.FileSystem,%20java.lang.String,%20java.lang.String)">downloadFileFromHDFS(TaskInputOutputContext, FileSystem, String, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#downloadGATKIndex(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20java.lang.String)">downloadGATKIndex(TaskInputOutputContext, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#downloadGFF(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20java.lang.String)">downloadGFF(TaskInputOutputContext, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#downloadSites(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20java.lang.String)">downloadSites(TaskInputOutputContext, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#downloadSTARIndex(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20java.lang.String,%20boolean)">downloadSTARIndex(TaskInputOutputContext, String, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#dryRun">dryRun</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html" title="class in be.ugent.intec.halvade.tools"><span class="strong">DummyAlignerInstance</span></a> - Class in <a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></dt>
-<dd>&nbsp;</dd>
-</dl>
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diff --git a/halvade/dist/javadoc/index-files/index-5.html b/halvade/dist/javadoc/index-files/index-5.html
deleted file mode 100644
index 66525ae..0000000
--- a/halvade/dist/javadoc/index-files/index-5.html
+++ /dev/null
@@ -1,129 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<!--   -->
-</a>
-<h2 class="title">E</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#elPrep(java.lang.String,%20java.lang.String,%20java.lang.String,%20int,%20boolean,%20java.lang.String,%20java.lang.String,%20java.lang.String)">elPrep(String, String, String, int, boolean, String, String, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#elPrepPreprocess(org.apache.hadoop.mapreduce.Reducer.Context,%20be.ugent.intec.halvade.tools.PreprocessingTools,%20be.ugent.intec.halvade.utils.SAMRecordIterator,%20java.lang.String)">elPrepPreprocess(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, PreprocessingTools, SAMRecordIterator, String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html#end">end</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.BedRegion.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter.BedRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Logger.html#EXCEPTION(java.lang.Exception)">EXCEPTION(Exception)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Logger.html" title="class in be.ugent.intec.halvade.utils">Logger</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#exportSplitter(java.lang.String,%20org.apache.hadoop.conf.Configuration)">exportSplitter(String, Configuration)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-</dl>
-<a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">K</a>&nbsp;<a href="index-12.html">L</a>&nbsp;<a href="index-13.html">M</a>&nbsp;<a href="index-14.html">N</a>&nbsp;<a href="index-15.html">O</a>&nbsp;<a href="index-16.html">P</a>&nbsp;<a href="index-17.html">Q</a>&nbsp;<a href="index-18.html">R</a>&nbsp;<a href="index-19.html">S</a>&nbsp;<a href="index-20.html">T</a>&nbsp;<a href="index-21.html">U</a>&nbsp;<a href="index-22.html">V</a>&nbsp;<a href="index-23.html">W</a>&nbsp;</div>
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diff --git a/halvade/dist/javadoc/index-files/index-6.html b/halvade/dist/javadoc/index-files/index-6.html
deleted file mode 100644
index f73f6d4..0000000
--- a/halvade/dist/javadoc/index-files/index-6.html
+++ /dev/null
@@ -1,173 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
-<head>
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-<body>
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-<!--   -->
-</a>
-<h2 class="title">F</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#f">f</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/CommandGenerator.html#featureCounts(java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20int,%20java.lang.String)">featureCounts(String, String, String, String, int, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/CommandGenerator.html" title="class in be.ugent.intec.halvade.utils">CommandGenerator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#feedLine(java.lang.String,%20be.ugent.intec.halvade.utils.ProcessBuilderWrapper)">feedLine(String, ProcessBuilderWrapper)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html#feedLine(java.lang.String,%20int)">feedLine(String, int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html" title="class in be.ugent.intec.halvade.tools">Bowtie2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html#feedLine(java.lang.String,%20int)">feedLine(String, int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">BWAAlnInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html#feedLine(java.lang.String)">feedLine(String)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html" title="class in be.ugent.intec.halvade.tools">BWAMemInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html#feedLine(java.lang.String,%20int)">feedLine(String, int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html" title="class in be.ugent.intec.halvade.tools">Cushaw2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#feedLine(java.lang.String,%20int,%20int)">feedLine(String, int, int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#file">file</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#filename">filename</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#filterBed">filterBed</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#filterBedFile">filterBedFile</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#filterDBsnp">filterDBsnp</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#filterDBSnp">filterDBSnp</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#filterDBSnps(java.lang.String,%20java.lang.String,%20be.ugent.intec.halvade.utils.ChromosomeRange,%20java.lang.String,%20int)">filterDBSnps(String, String, ChromosomeRange, String, int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#filterExomeBed(java.lang.String,%20be.ugent.intec.halvade.utils.ChromosomeRange)">filterExomeBed(String, ChromosomeRange)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#filterVariants(org.apache.hadoop.mapreduce.Reducer.Context,%20java.lang.String,%20be.ugent.intec.halvade.tools.GATKTools,%20java.lang.String,%20java.lang.String)">filterVariants(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, String, GATKTools, String, String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#findFile(java.lang.String,%20java.lang.String,%20boolean)">findFile(String, String, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/QualityEncoding.html#fixMisencodedQuals(htsjdk.samtools.SAMRecord)">fixMisencodedQuals(SAMRecord)</a></span> - Static method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/QualityEncoding.html" title="class in be.ugent.intec.halvade.tools">QualityEncoding</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#flushStream()">flushStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html#flushStream()">flushStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html" title="class in be.ugent.intec.halvade.tools">Bowtie2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html#flushStream()">flushStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">BWAAlnInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html#flushStream()">flushStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html" title="class in be.ugent.intec.halvade.tools">BWAMemInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html#flushStream()">flushStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html" title="class in be.ugent.intec.halvade.tools">Cushaw2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html#flushStream()">flushStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html" title="class in be.ugent.intec.halvade.tools">DummyAlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#flushStream()">flushStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#forceWrite(java.nio.ByteBuffer)">forceWrite(ByteBuffer)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
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diff --git a/halvade/dist/javadoc/index-files/index-7.html b/halvade/dist/javadoc/index-files/index-7.html
deleted file mode 100644
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--- a/halvade/dist/javadoc/index-files/index-7.html
+++ /dev/null
@@ -1,363 +0,0 @@
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-<!--   -->
-</a>
-<h2 class="title">G</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#GATK_REF_FILES">GATK_REF_FILES</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">GATKReducer</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#GATKReducer()">GATKReducer()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools"><span class="strong">GATKTools</span></a> - Class in <a href="../be/ugent/intec/halvade/tools/package-summary.html">be.ugent.intec.halvade.tools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#GATKTools(java.lang.String,%20java.lang.String)">GATKTools(String, String)</a></span> - Constructor for class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes"><span class="strong">GenomeSJ</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/datatypes/package-summary.html">be.ugent.intec.halvade.hadoop.datatypes</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html#GenomeSJ()">GenomeSJ()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">GenomeSJ</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/partitioners/GenomeSJGroupingComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners"><span class="strong">GenomeSJGroupingComparator</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/partitioners/package-summary.html">be.ugent.intec.halvade.hadoop.partitioners</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/partitioners/GenomeSJGroupingComparator.html#GenomeSJGroupingComparator()">GenomeSJGroupingComparator()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.partitioners.<a href="../be/ugent/intec/halvade/hadoop/partitioners/GenomeSJGroupingComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners">GenomeSJGroupingComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/partitioners/GenomeSJSortComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners"><span class="strong">GenomeSJSortComparator</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/partitioners/package-summary.html">be.ugent.intec.halvade.hadoop.partitioners</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/partitioners/GenomeSJSortComparator.html#GenomeSJSortComparator()">GenomeSJSortComparator()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.partitioners.<a href="../be/ugent/intec/halvade/hadoop/partitioners/GenomeSJSortComparator.html" title="class in be.ugent.intec.halvade.hadoop.partitioners">GenomeSJSortComparator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html#getAlignmentEnd()">getAlignmentEnd()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html#getAlignmentStart()">getAlignmentStart()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getBed(org.apache.hadoop.conf.Configuration)">getBed(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html#getBedRegion()">getBedRegion()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange.Range</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getBedRegions(org.apache.hadoop.conf.Configuration)">getBedRegions(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html#getBowtie2Instance(org.apache.hadoop.mapreduce.Mapper.Context,%20java.lang.String)">getBowtie2Instance(Mapper.Context, String)</a></span> - Static method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html" title="class in be.ugent.intec.halvade.tools">Bowtie2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html#getBWAInstance(org.apache.hadoop.mapreduce.Mapper.Context,%20java.lang.String)">getBWAInstance(Mapper.Context, String)</a></span> - Static method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">BWAAlnInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html#getBWAInstance(org.apache.hadoop.mapreduce.Mapper.Context,%20java.lang.String)">getBWAInstance(Mapper.Context, String)</a></span> - Static method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html" title="class in be.ugent.intec.halvade.tools">BWAMemInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getChrList(org.apache.hadoop.conf.Configuration)">getChrList(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html#getChromosome()">getChromosome()</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#getChromosomeRange()">getChromosomeRange()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#getCount()">getCount()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Timer.html#getCurrentTime()">getCurrentTime()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Timer.html" title="class in be.ugent.intec.halvade.utils">Timer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html#getCushaw2Instance(org.apache.hadoop.mapreduce.Mapper.Context,%20java.lang.String)">getCushaw2Instance(Mapper.Context, String)</a></span> - Static method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html" title="class in be.ugent.intec.halvade.tools">Cushaw2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getCustomArgs(org.apache.hadoop.conf.Configuration,%20java.lang.String,%20java.lang.String)">getCustomArgs(Configuration, String, String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html#getDummyInstance(org.apache.hadoop.mapreduce.Mapper.Context,%20java.lang.String)">getDummyInstance(Mapper.Context, String)</a></span> - Static method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html" title="class in be.ugent.intec.halvade.tools">DummyAlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Timer.html#getElapsedTime()">getElapsedTime()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Timer.html" title="class in be.ugent.intec.halvade.utils">Timer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#getExecutionTime()">getExecutionTime()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#getExitState()">getExitState()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#getFileHeader()">getFileHeader()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html#getFileName(java.lang.String,%20java.lang.String,%20int)">getFileName(String, String, int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html" title="class in be.ugent.intec.halvade.tools">Bowtie2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html#getFileName(java.lang.String,%20java.lang.String,%20boolean,%20int)">getFileName(String, String, boolean, int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">BWAAlnInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html#getFileName(java.lang.String,%20java.lang.String,%20int)">getFileName(String, String, int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html" title="class in be.ugent.intec.halvade.tools">Cushaw2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#getFileName(java.lang.String,%20java.lang.String,%20int)">getFileName(String, String, int)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getFilterBed(org.apache.hadoop.conf.Configuration)">getFilterBed(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getFilterDBSnp(org.apache.hadoop.conf.Configuration)">getFilterDBSnp(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Timer.html#getFormattedCurrentTime()">getFormattedCurrentTime()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Timer.html" title="class in be.ugent.intec.halvade.utils">Timer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Timer.html#getFormattedElapsedTime()">getFormattedElapsedTime()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Timer.html" title="class in be.ugent.intec.halvade.utils">Timer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#getGenomeDir()">getGenomeDir()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getGff(org.apache.hadoop.conf.Configuration)">getGff(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Timer.html#getGlobalTime()">getGlobalTime()</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Timer.html" title="class in be.ugent.intec.halvade.utils">Timer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getHeaderFile(org.apache.hadoop.conf.Configuration)">getHeaderFile(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#getIdleCores(org.apache.hadoop.mapreduce.Mapper.Context)">getIdleCores(Mapper.Context)</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getInputDir(org.apache.hadoop.conf.Configuration)">getInputDir(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#getInputSize(java.lang.String,%20org.apache.hadoop.conf.Configuration)">getInputSize(String, Configuration)</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getIsPaired(org.apache.hadoop.conf.Configuration)">getIsPaired(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getIsPass2(org.apache.hadoop.conf.Configuration)">getIsPass2(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getIsRNA(org.apache.hadoop.conf.Configuration)">getIsRNA(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/GATKTools.html#getJava()">getJava()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/GATKTools.html" title="class in be.ugent.intec.halvade.tools">GATKTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html#getJava()">getJava()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/PreprocessingTools.html" title="class in be.ugent.intec.halvade.tools">PreprocessingTools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getJava(org.apache.hadoop.conf.Configuration)">getJava(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getkeepChrSplitPairs(org.apache.hadoop.conf.Configuration)">getkeepChrSplitPairs(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getKeepDups(org.apache.hadoop.conf.Configuration)">getKeepDups(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getKeepFiles(org.apache.hadoop.conf.Configuration)">getKeepFiles(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getKnownSitesOnHDFS(org.apache.hadoop.conf.Configuration)">getKnownSitesOnHDFS(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#getLine(org.apache.hadoop.fs.FSDataInputStream)">getLine(FSDataInputStream)</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#getLock()">getLock()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getMapContainerCount(org.apache.hadoop.conf.Configuration)">getMapContainerCount(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getMapTasksLeft(org.apache.hadoop.conf.Configuration)">getMapTasksLeft(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getMapThreads(org.apache.hadoop.conf.Configuration)">getMapThreads(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getMergeBam(org.apache.hadoop.conf.Configuration)">getMergeBam(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getMinChrLength(org.apache.hadoop.conf.Configuration)">getMinChrLength(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getNumberOfFiles(org.apache.hadoop.conf.Configuration)">getNumberOfFiles(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#GetOptions(java.lang.String[],%20org.apache.hadoop.conf.Configuration)">GetOptions(String[], Configuration)</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getOutDir(org.apache.hadoop.conf.Configuration)">getOutDir(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#getOverhang()">getOverhang()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgPartitioner.html#getPartition(be.ugent.intec.halvade.hadoop.datatypes.ChromosomeRegion,%20org.seqdoop.hadoop_bam.SAMRecordWritable,%20int)">getPartition(ChromosomeRegion, SAMRecordWritable, int)</a></span> - Method in class be.ugent.intec.halvade.hadoop.partitioners.<a href="../be/ugent/intec/halvade/hadoop/partitioners/ChrRgPartitioner.html" title="class in be.ugent.intec.halvade.hadoop.partitioners">ChrRgPartitioner</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html#getPicardRegion()">getPicardRegion()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeRange.Range.html" title="class in be.ugent.intec.halvade.utils">ChromosomeRange.Range</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html#getPosition()">getPosition()</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#getProgramNames()">getProgramNames()</a></span> - Method in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getReadGroup(org.apache.hadoop.conf.Configuration)">getReadGroup(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#getReadGroupData(org.apache.hadoop.conf.Configuration)">getReadGroupData(Configuration)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#getReadGroupData(org.apache.hadoop.conf.Configuration)">getReadGroupData(Configuration)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#getReadsPerContig(java.util.List,%20java.lang.String)">getReadsPerContig(List&lt;ChromosomeSplitter.BedRegion&gt;, String)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getRedistribute(org.apache.hadoop.conf.Configuration)">getRedistribute(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html#getReduceNumber()">getReduceNumber()</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">ChromosomeRegion</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getReducerThreads(org.apache.hadoop.conf.Configuration)">getReducerThreads(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getRefDirOnScratch(org.apache.hadoop.conf.Configuration)">getRefDirOnScratch(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getRefOnHDFS(org.apache.hadoop.conf.Configuration)">getRefOnHDFS(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getRefSize(org.apache.hadoop.conf.Configuration)">getRefSize(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#getRegionCount()">getRegionCount()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#getRegionLength()">getRegionLength()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#getRegions(htsjdk.samtools.SAMRecord,%20int,%20int)">getRegions(SAMRecord, int, int)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html#getRegions(htsjdk.samtools.SAMRecord,%20int)">getRegions(SAMRecord, int)</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ChromosomeSplitter.html" title="class in be.ugent.intec.halvade.utils">ChromosomeSplitter</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getReportAllVariant(org.apache.hadoop.conf.Configuration)">getReportAllVariant(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getSCC(org.apache.hadoop.conf.Configuration,%20boolean)">getSCC(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getScratchTempDir(org.apache.hadoop.conf.Configuration)">getScratchTempDir(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getSEC(org.apache.hadoop.conf.Configuration,%20boolean)">getSEC(Configuration, boolean)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html#getSecKey()">getSecKey()</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">GenomeSJ</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getSequenceDictionary(org.apache.hadoop.conf.Configuration)">getSequenceDictionary(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getStarDirOnHDFS(org.apache.hadoop.conf.Configuration)">getStarDirOnHDFS(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getStarDirPass2HDFS(org.apache.hadoop.conf.Configuration)">getStarDirPass2HDFS(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#getSTARInstance(org.apache.hadoop.mapreduce.Mapper.Context,%20java.lang.String,%20int)">getSTARInstance(Mapper.Context, String, int)</a></span> - Static method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#getState()">getState()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html#getState()">getState()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html" title="class in be.ugent.intec.halvade.tools">Bowtie2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html#getState()">getState()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">BWAAlnInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html#getState()">getState()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html" title="class in be.ugent.intec.halvade.tools">BWAMemInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html#getState()">getState()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html" title="class in be.ugent.intec.halvade.tools">Cushaw2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html#getState()">getState()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html" title="class in be.ugent.intec.halvade.tools">DummyAlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#getState()">getState()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#getState()">getState()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#getSTDERRStream()">getSTDERRStream()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#getSTDINStream()">getSTDINStream()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#getSTDINWriter()">getSTDINWriter()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#getSTDOUTStream()">getSTDOUTStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html#getSTDOUTStream()">getSTDOUTStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Bowtie2Instance.html" title="class in be.ugent.intec.halvade.tools">Bowtie2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html#getSTDOUTStream()">getSTDOUTStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAAlnInstance.html" title="class in be.ugent.intec.halvade.tools">BWAAlnInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html#getSTDOUTStream()">getSTDOUTStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/BWAMemInstance.html" title="class in be.ugent.intec.halvade.tools">BWAMemInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html#getSTDOUTStream()">getSTDOUTStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/Cushaw2Instance.html" title="class in be.ugent.intec.halvade.tools">Cushaw2Instance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html#getSTDOUTStream()">getSTDOUTStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/DummyAlignerInstance.html" title="class in be.ugent.intec.halvade.tools">DummyAlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/STARInstance.html#getSTDOUTStream()">getSTDOUTStream()</a></span> - Method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/STARInstance.html" title="class in be.ugent.intec.halvade.tools">STARInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#getSTDOUTStream()">getSTDOUTStream()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html#getType()">getType()</a></span> - Method in class be.ugent.intec.halvade.hadoop.datatypes.<a href="../be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.html" title="class in be.ugent.intec.halvade.hadoop.datatypes">GenomeSJ</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getUpdateReadGroup(org.apache.hadoop.conf.Configuration)">getUpdateReadGroup(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getUseElPrep(org.apache.hadoop.conf.Configuration)">getUseElPrep(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getUseUnifiedGenotyper(org.apache.hadoop.conf.Configuration)">getUseUnifiedGenotyper(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#getVcores(org.apache.hadoop.conf.Configuration)">getVcores(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#gff">gff</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#gff">gff</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#GFF_LOCK">GFF_LOCK</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/QualityEncoding.html#guessEncoding(htsjdk.samtools.SAMRecord)">guessEncoding(SAMRecord)</a></span> - Static method in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/QualityEncoding.html" title="class in be.ugent.intec.halvade.tools">QualityEncoding</a></dt>
-<dd>&nbsp;</dd>
-</dl>
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diff --git a/halvade/dist/javadoc/index-files/index-8.html b/halvade/dist/javadoc/index-files/index-8.html
deleted file mode 100644
index c98f205..0000000
--- a/halvade/dist/javadoc/index-files/index-8.html
+++ /dev/null
@@ -1,195 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<!--   -->
-</a>
-<h2 class="title">H</h2>
-<dl>
-<dt><a href="../be/ugent/intec/halvade/Halvade.html" title="class in be.ugent.intec.halvade"><span class="strong">Halvade</span></a> - Class in <a href="../be/ugent/intec/halvade/package-summary.html">be.ugent.intec.halvade</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/Halvade.html#Halvade()">Halvade()</a></span> - Constructor for class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/Halvade.html" title="class in be.ugent.intec.halvade">Halvade</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#HALVADE_BOWTIE2_SUFFIX">HALVADE_BOWTIE2_SUFFIX</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#HALVADE_BWA_SUFFIX">HALVADE_BWA_SUFFIX</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#HALVADE_CUSHAW2_SUFFIX">HALVADE_CUSHAW2_SUFFIX</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#HALVADE_DBSNP_SUFFIX">HALVADE_DBSNP_SUFFIX</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#HALVADE_GATK_SUFFIX">HALVADE_GATK_SUFFIX</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#HALVADE_STAR_SUFFIX_P1">HALVADE_STAR_SUFFIX_P1</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#HALVADE_STAR_SUFFIX_P2">HALVADE_STAR_SUFFIX_P2</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#halvadeBinaries">halvadeBinaries</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">HalvadeConf</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#HalvadeConf()">HalvadeConf()</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeCounters.html" title="enum in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">HalvadeCounters</span></a> - Enum in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">HalvadeFileLock</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html#HalvadeFileLock(org.apache.hadoop.mapreduce.TaskInputOutputContext,%20java.lang.String,%20java.lang.String)">HalvadeFileLock(TaskInputOutputContext, String, String)</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileLock.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileLock</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils"><span class="strong">HalvadeFileUtils</span></a> - Class in <a href="../be/ugent/intec/halvade/utils/package-summary.html">be.ugent.intec.halvade.utils</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html#HalvadeFileUtils()">HalvadeFileUtils()</a></span> - Constructor for class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeFileUtils.html" title="class in be.ugent.intec.halvade.utils">HalvadeFileUtils</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">HalvadeMapper</span></a>&lt;<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="type parameter in HalvadeMapper">T1</a>,<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="type parameter in HalvadeMapper">T2</a>&gt; - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html#HalvadeMapper()">HalvadeMapper()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade"><span class="strong">HalvadeOptions</span></a> - Class in <a href="../be/ugent/intec/halvade/package-summary.html">be.ugent.intec.halvade</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#HalvadeOptions()">HalvadeOptions()</a></span> - Constructor for class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/MapReduceRunner.html#halvadeOpts">halvadeOpts</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/MapReduceRunner.html" title="class in be.ugent.intec.halvade">MapReduceRunner</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">HalvadeReducer</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#HalvadeReducer()">HalvadeReducer()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade"><span class="strong">HalvadeResourceManager</span></a> - Class in <a href="../be/ugent/intec/halvade/package-summary.html">be.ugent.intec.halvade</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeResourceManager.html#HalvadeResourceManager()">HalvadeResourceManager()</a></span> - Constructor for class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeResourceManager.html" title="class in be.ugent.intec.halvade">HalvadeResourceManager</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeTextInputFormat.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">HalvadeTextInputFormat</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeTextInputFormat.html#HalvadeTextInputFormat()">HalvadeTextInputFormat()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeTextInputFormat.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeTextInputFormat</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#hasNext()">hasNext()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#hdfsSites">hdfsSites</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#header">header</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#header">header</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#header">header</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#header">header</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">HTSeqCombineMapper</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineMapper.html#HTSeqCombineMapper()">HTSeqCombineMapper()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HTSeqCombineMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce"><span class="strong">HTSeqCombineReducer</span></a> - Class in <a href="../be/ugent/intec/halvade/hadoop/mapreduce/package-summary.html">be.ugent.intec.halvade.hadoop.mapreduce</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineReducer.html#HTSeqCombineReducer()">HTSeqCombineReducer()</a></span> - Constructor for class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HTSeqCombineReducer</a></dt>
-<dd>&nbsp;</dd>
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diff --git a/halvade/dist/javadoc/index-files/index-9.html b/halvade/dist/javadoc/index-files/index-9.html
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-<!--   -->
-</a>
-<h2 class="title">I</h2>
-<dl>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/HalvadeOptions.html#in">in</a></span> - Variable in class be.ugent.intec.halvade.<a href="../be/ugent/intec/halvade/HalvadeOptions.html" title="class in be.ugent.intec.halvade">HalvadeOptions</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#indelRealignment(org.apache.hadoop.mapreduce.Reducer.Context,%20java.lang.String,%20be.ugent.intec.halvade.tools.GATKTools,%20java.lang.String,%20java.lang.String)">indelRealignment(Reducer&lt;ChromosomeRegion, SAMRecordWritable, ChromosomeRegion, VariantContextWritable&gt;.Context, String, GATKTools, String, String)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/Logger.html#INFO(java.lang.String)">INFO(String)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/Logger.html" title="class in be.ugent.intec.halvade.utils">Logger</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html#inputIsBam">inputIsBam</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">BamMergeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html#inputIsBam">inputIsBam</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/HalvadeConf.html#inputIsBam(org.apache.hadoop.conf.Configuration)">inputIsBam(Configuration)</a></span> - Static method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/HalvadeConf.html" title="class in be.ugent.intec.halvade.utils">HalvadeConf</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/AlignedBamMapper.html#instance">instance</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/AlignedBamMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">AlignedBamMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html#instance">instance</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeMapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#INTERVAL_OVERLAP">INTERVAL_OVERLAP</a></span> - Static variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html#isAlive()">isAlive()</a></span> - Method in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/ProcessBuilderWrapper.html" title="class in be.ugent.intec.halvade.utils">ProcessBuilderWrapper</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#isFirstAttempt">isFirstAttempt</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/tools/AlignerInstance.html#isPaired">isPaired</a></span> - Variable in class be.ugent.intec.halvade.tools.<a href="../be/ugent/intec/halvade/tools/AlignerInstance.html" title="class in be.ugent.intec.halvade.tools">AlignerInstance</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html#isRNA">isRNA</a></span> - Variable in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">GATKReducer</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeTextInputFormat.html#isSplitable(org.apache.hadoop.mapreduce.JobContext,%20org.apache.hadoop.fs.Path)">isSplitable(JobContext, Path)</a></span> - Method in class be.ugent.intec.halvade.hadoop.mapreduce.<a href="../be/ugent/intec/halvade/hadoop/mapreduce/HalvadeTextInputFormat.html" title="class in be.ugent.intec.halvade.hadoop.mapreduce">HalvadeTextInputFormat</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="strong"><a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html#it">it</a></span> - Variable in class be.ugent.intec.halvade.utils.<a href="../be/ugent/intec/halvade/utils/SAMRecordIterator.html" title="class in be.ugent.intec.halvade.utils">SAMRecordIterator</a></dt>
-<dd>&nbsp;</dd>
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