bugfix in resourcemanager

ddcap · Feb 14, 2016 · 095d449 · 095d449
1 parent 5493be6
commit 095d449
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diff --git a/halvade/build/built-jar.properties b/halvade/build/built-jar.properties
diff --git a/halvade/build/classes/be/ugent/intec/halvade/Halvade.class b/halvade/build/classes/be/ugent/intec/halvade/Halvade.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/HalvadeOptions.class b/halvade/build/classes/be/ugent/intec/halvade/HalvadeOptions.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/HalvadeResourceManager.class b/halvade/build/classes/be/ugent/intec/halvade/HalvadeResourceManager.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/MapReduceRunner.class b/halvade/build/classes/be/ugent/intec/halvade/MapReduceRunner.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/datatypes/ChromosomeRegion.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/datatypes/GenomeSJ.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/AlignedBamMapper.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/AlignedBamMapper.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/BWAAlnMapper.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/BWAAlnMapper.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/BWAMemMapper.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/BWAMemMapper.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/BamMergeReducer.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/Bowtie2Mapper.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/Bowtie2Mapper.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/CountReadsReducer.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/CountReadsReducer.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/Cushaw2Mapper.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/Cushaw2Mapper.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/DnaGATKReducer.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/DnaGATKReducer.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/GATKReducer.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineMapper.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineMapper.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineReducer.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/HTSeqCombineReducer.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/HalvadeCounters.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/HalvadeCounters.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/HalvadeMapper.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/HalvadeTextInputFormat.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/HalvadeTextInputFormat.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/RebuildStarGenomeReducer.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/RnaGATKReducer.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/RnaGATKReducer.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/StarAlignPassXMapper.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineMapper.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineMapper.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/mapreduce/VCFCombineReducer.class
diff --git a/...de/build/classes/be/ugent/intec/halvade/hadoop/partitioners/ChrRgGroupingComparator.class b/...de/build/classes/be/ugent/intec/halvade/hadoop/partitioners/ChrRgGroupingComparator.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/partitioners/ChrRgPartitioner.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/partitioners/ChrRgPartitioner.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/hadoop/partitioners/ChrRgSortComparator.class b/halvade/build/classes/be/ugent/intec/halvade/hadoop/partitioners/ChrRgSortComparator.class
diff --git a/...build/classes/be/ugent/intec/halvade/hadoop/partitioners/GenomeSJGroupingComparator.class b/...build/classes/be/ugent/intec/halvade/hadoop/partitioners/GenomeSJGroupingComparator.class
diff --git a/...ade/build/classes/be/ugent/intec/halvade/hadoop/partitioners/GenomeSJSortComparator.class b/...ade/build/classes/be/ugent/intec/halvade/hadoop/partitioners/GenomeSJSortComparator.class
diff --git a/.../build/classes/be/ugent/intec/halvade/hadoop/partitioners/SimpleChrRegionComparator.class b/.../build/classes/be/ugent/intec/halvade/hadoop/partitioners/SimpleChrRegionComparator.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/AlignerInstance.class b/halvade/build/classes/be/ugent/intec/halvade/tools/AlignerInstance.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/BWAAlnInstance.class b/halvade/build/classes/be/ugent/intec/halvade/tools/BWAAlnInstance.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/BWAMemInstance.class b/halvade/build/classes/be/ugent/intec/halvade/tools/BWAMemInstance.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/Bowtie2Instance.class b/halvade/build/classes/be/ugent/intec/halvade/tools/Bowtie2Instance.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/Cushaw2Instance.class b/halvade/build/classes/be/ugent/intec/halvade/tools/Cushaw2Instance.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/DummyAlignerInstance.class b/halvade/build/classes/be/ugent/intec/halvade/tools/DummyAlignerInstance.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/GATKTools.class b/halvade/build/classes/be/ugent/intec/halvade/tools/GATKTools.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/PreprocessingTools.class b/halvade/build/classes/be/ugent/intec/halvade/tools/PreprocessingTools.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/ProcessException.class b/halvade/build/classes/be/ugent/intec/halvade/tools/ProcessException.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/QualityEncoding$QENCODING.class b/halvade/build/classes/be/ugent/intec/halvade/tools/QualityEncoding$QENCODING.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/QualityEncoding.class b/halvade/build/classes/be/ugent/intec/halvade/tools/QualityEncoding.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/QualityException.class b/halvade/build/classes/be/ugent/intec/halvade/tools/QualityException.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/tools/STARInstance.class b/halvade/build/classes/be/ugent/intec/halvade/tools/STARInstance.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/ChromosomeRange$Range.class b/halvade/build/classes/be/ugent/intec/halvade/utils/ChromosomeRange$Range.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/ChromosomeRange.class b/halvade/build/classes/be/ugent/intec/halvade/utils/ChromosomeRange.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/ChromosomeSplitter$1.class b/halvade/build/classes/be/ugent/intec/halvade/utils/ChromosomeSplitter$1.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/ChromosomeSplitter$BedRegion.class b/halvade/build/classes/be/ugent/intec/halvade/utils/ChromosomeSplitter$BedRegion.class
diff --git a/...e/build/classes/be/ugent/intec/halvade/utils/ChromosomeSplitter$BedRegionComparator.class b/...e/build/classes/be/ugent/intec/halvade/utils/ChromosomeSplitter$BedRegionComparator.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/ChromosomeSplitter$KeyCountPair.class b/halvade/build/classes/be/ugent/intec/halvade/utils/ChromosomeSplitter$KeyCountPair.class
diff --git a/...uild/classes/be/ugent/intec/halvade/utils/ChromosomeSplitter$KeyCountPairComparator.class b/...uild/classes/be/ugent/intec/halvade/utils/ChromosomeSplitter$KeyCountPairComparator.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/ChromosomeSplitter.class b/halvade/build/classes/be/ugent/intec/halvade/utils/ChromosomeSplitter.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/CommandGenerator.class b/halvade/build/classes/be/ugent/intec/halvade/utils/CommandGenerator.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/HalvadeConf.class b/halvade/build/classes/be/ugent/intec/halvade/utils/HalvadeConf.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/HalvadeFileLock.class b/halvade/build/classes/be/ugent/intec/halvade/utils/HalvadeFileLock.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/HalvadeFileUtils.class b/halvade/build/classes/be/ugent/intec/halvade/utils/HalvadeFileUtils.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/Logger.class b/halvade/build/classes/be/ugent/intec/halvade/utils/Logger.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/ProcessBuilderWrapper$ProcMon.class b/halvade/build/classes/be/ugent/intec/halvade/utils/ProcessBuilderWrapper$ProcMon.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/ProcessBuilderWrapper.class b/halvade/build/classes/be/ugent/intec/halvade/utils/ProcessBuilderWrapper.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/SAMRecordIterator.class b/halvade/build/classes/be/ugent/intec/halvade/utils/SAMRecordIterator.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/SAMStreamHandler.class b/halvade/build/classes/be/ugent/intec/halvade/utils/SAMStreamHandler.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/StreamGobbler.class b/halvade/build/classes/be/ugent/intec/halvade/utils/StreamGobbler.class
diff --git a/halvade/build/classes/be/ugent/intec/halvade/utils/Timer.class b/halvade/build/classes/be/ugent/intec/halvade/utils/Timer.class
diff --git a/halvade/dist/Halvade.jar b/halvade/dist/Halvade.jar
diff --git a/halvade/dist/HalvadeWithLibs.jar b/halvade/dist/HalvadeWithLibs.jar
diff --git a/halvade/dist/javadoc/allclasses-frame.html b/halvade/dist/javadoc/allclasses-frame.html
diff --git a/halvade/dist/javadoc/allclasses-noframe.html b/halvade/dist/javadoc/allclasses-noframe.html