diff --git a/nbproject/build-impl.xml b/nbproject/build-impl.xml
index f09872d..d88f591 100644
--- a/nbproject/build-impl.xml
+++ b/nbproject/build-impl.xml
@@ -71,8 +71,8 @@ is divided into following sections:
         <property file="${user.properties.file}"/>
         <!-- The two properties below are usually overridden -->
         <!-- by the active platform. Just a fallback. -->
-        <property name="default.javac.source" value="1.4"/>
-        <property name="default.javac.target" value="1.4"/>
+        <property name="default.javac.source" value="1.6"/>
+        <property name="default.javac.target" value="1.6"/>
     </target>
     <target depends="-pre-init,-init-private,-init-libraries,-init-user" name="-init-project">
         <property file="nbproject/configs/${config}.properties"/>
@@ -101,7 +101,7 @@ is divided into following sections:
             <and>
                 <isset property="javac.profile"/>
                 <length length="0" string="${javac.profile}" when="greater"/>
-                <matches pattern="1\.[89](\..*)?" string="${javac.source}"/>
+                <matches pattern="((1\.[89])|9)(\..*)?" string="${javac.source}"/>
             </and>
         </condition>
         <condition property="do.archive">
@@ -181,6 +181,7 @@ is divided into following sections:
         <property name="application.args" value=""/>
         <property name="source.encoding" value="${file.encoding}"/>
         <property name="runtime.encoding" value="${source.encoding}"/>
+        <property name="manifest.encoding" value="${source.encoding}"/>
         <condition property="javadoc.encoding.used" value="${javadoc.encoding}">
             <and>
                 <isset property="javadoc.encoding"/>
@@ -216,7 +217,12 @@ is divided into following sections:
                 </not>
             </and>
         </condition>
-        <property name="javac.fork" value="${jdkBug6558476}"/>
+        <condition else="false" property="javac.fork">
+            <or>
+                <istrue value="${jdkBug6558476}"/>
+                <istrue value="${javac.external.vm}"/>
+            </or>
+        </condition>
         <property name="jar.index" value="false"/>
         <property name="jar.index.metainf" value="${jar.index}"/>
         <property name="copylibs.rebase" value="true"/>
@@ -242,6 +248,7 @@ is divided into following sections:
         <condition else="" property="testng.debug.mode" value="-mixed">
             <istrue value="${junit+testng.available}"/>
         </condition>
+        <property name="java.failonerror" value="true"/>
     </target>
     <target name="-post-init">
         <!-- Empty placeholder for easier customization. -->
@@ -718,7 +725,7 @@ is divided into following sections:
             <sequential>
                 <property environment="env"/>
                 <resolve name="profiler.current.path" value="${profiler.info.pathvar}"/>
-                <java classname="@{classname}" dir="${profiler.info.dir}" fork="true" jvm="${profiler.info.jvm}">
+                <java classname="@{classname}" dir="${profiler.info.dir}" failonerror="${java.failonerror}" fork="true" jvm="${profiler.info.jvm}">
                     <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
                     <jvmarg value="${profiler.info.jvmargs.agent}"/>
                     <jvmarg line="${profiler.info.jvmargs}"/>
@@ -793,7 +800,7 @@ is divided into following sections:
             <attribute default="${debug.classpath}" name="classpath"/>
             <element name="customize" optional="true"/>
             <sequential>
-                <java classname="@{classname}" dir="${work.dir}" fork="true">
+                <java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true">
                     <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
                     <jvmarg line="${debug-args-line}"/>
                     <jvmarg value="-Xrunjdwp:transport=${debug-transport},address=${jpda.address}"/>
@@ -820,7 +827,7 @@ is divided into following sections:
             <attribute default="jvm" name="jvm"/>
             <element name="customize" optional="true"/>
             <sequential>
-                <java classname="@{classname}" dir="${work.dir}" fork="true">
+                <java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true">
                     <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
                     <jvmarg value="-Dfile.encoding=${runtime.encoding}"/>
                     <redirector errorencoding="${runtime.encoding}" inputencoding="${runtime.encoding}" outputencoding="${runtime.encoding}"/>
@@ -859,7 +866,7 @@ is divided into following sections:
                     </chainedmapper>
                 </pathconvert>
                 <taskdef classname="org.netbeans.modules.java.j2seproject.copylibstask.CopyLibs" classpath="${libs.CopyLibs.classpath}" name="copylibs"/>
-                <copylibs compress="${jar.compress}" excludeFromCopy="${copylibs.excludes}" index="${jar.index}" indexMetaInf="${jar.index.metainf}" jarfile="${dist.jar}" manifest="@{manifest}" rebase="${copylibs.rebase}" runtimeclasspath="${run.classpath.without.build.classes.dir}">
+                <copylibs compress="${jar.compress}" excludeFromCopy="${copylibs.excludes}" index="${jar.index}" indexMetaInf="${jar.index.metainf}" jarfile="${dist.jar}" manifest="@{manifest}" manifestencoding="UTF-8" rebase="${copylibs.rebase}" runtimeclasspath="${run.classpath.without.build.classes.dir}">
                     <fileset dir="${build.classes.dir}" excludes="${dist.archive.excludes}"/>
                     <manifest>
                         <attribute name="Class-Path" value="${jar.classpath}"/>
@@ -871,7 +878,7 @@ is divided into following sections:
     </target>
     <target name="-init-presetdef-jar">
         <presetdef name="jar" uri="http://www.netbeans.org/ns/j2se-project/1">
-            <jar compress="${jar.compress}" index="${jar.index}" jarfile="${dist.jar}">
+            <jar compress="${jar.compress}" index="${jar.index}" jarfile="${dist.jar}" manifestencoding="UTF-8">
                 <j2seproject1:fileset dir="${build.classes.dir}" excludes="${dist.archive.excludes}"/>
             </jar>
         </presetdef>
@@ -994,15 +1001,15 @@ is divided into following sections:
     </target>
     <target depends="init" if="do.archive+manifest.available" name="-do-jar-copy-manifest">
         <tempfile deleteonexit="true" destdir="${build.dir}" property="tmp.manifest.file"/>
-        <copy file="${manifest.file}" tofile="${tmp.manifest.file}"/>
+        <copy encoding="${manifest.encoding}" file="${manifest.file}" outputencoding="UTF-8" tofile="${tmp.manifest.file}"/>
     </target>
     <target depends="init,-do-jar-create-manifest,-do-jar-copy-manifest" if="do.archive+main.class.available" name="-do-jar-set-mainclass">
-        <manifest file="${tmp.manifest.file}" mode="update">
+        <manifest encoding="UTF-8" file="${tmp.manifest.file}" mode="update">
             <attribute name="Main-Class" value="${main.class}"/>
         </manifest>
     </target>
     <target depends="init,-do-jar-create-manifest,-do-jar-copy-manifest" if="do.archive+profile.available" name="-do-jar-set-profile">
-        <manifest file="${tmp.manifest.file}" mode="update">
+        <manifest encoding="UTF-8" file="${tmp.manifest.file}" mode="update">
             <attribute name="Profile" value="${javac.profile}"/>
         </manifest>
     </target>
@@ -1010,7 +1017,7 @@ is divided into following sections:
         <basename file="${application.splash}" property="splashscreen.basename"/>
         <mkdir dir="${build.classes.dir}/META-INF"/>
         <copy failonerror="false" file="${application.splash}" todir="${build.classes.dir}/META-INF"/>
-        <manifest file="${tmp.manifest.file}" mode="update">
+        <manifest encoding="UTF-8" file="${tmp.manifest.file}" mode="update">
             <attribute name="SplashScreen-Image" value="META-INF/${splashscreen.basename}"/>
         </manifest>
     </target>
@@ -1205,7 +1212,7 @@ is divided into following sections:
     <target depends="-profile-check" description="Profile a selected class in the IDE." if="profiler.configured" name="profile-test-with-main">
         <fail unless="run.class">Must select one file in the IDE or set run.class</fail>
         <startprofiler/>
-        <antcal target="run-test-with-main"/>
+        <antcall target="run-test-with-main"/>
     </target>
     <target depends="-profile-check,-profile-applet-pre72" if="profiler.configured" name="profile-applet" unless="profiler.info.jvmargs.agent">
         <fail unless="applet.url">Must select one file in the IDE or set applet.url</fail>
diff --git a/nbproject/genfiles.properties b/nbproject/genfiles.properties
index e5b83ba..1293f1b 100644
--- a/nbproject/genfiles.properties
+++ b/nbproject/genfiles.properties
@@ -4,5 +4,5 @@ build.xml.stylesheet.CRC32=8064a381@1.75.2.48
 # This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
 # Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
 nbproject/build-impl.xml.data.CRC32=91437f43
-nbproject/build-impl.xml.script.CRC32=097bff4d
-nbproject/build-impl.xml.stylesheet.CRC32=876e7a8f@1.75.2.48
+nbproject/build-impl.xml.script.CRC32=9ddad943
+nbproject/build-impl.xml.stylesheet.CRC32=830a3534@1.80.1.48
diff --git a/src/libra/common/hadoop/io/reader/sequence/RawReadReader.java b/src/libra/common/hadoop/io/reader/sequence/RawReadReader.java
index e362a7b..f3d5696 100644
--- a/src/libra/common/hadoop/io/reader/sequence/RawReadReader.java
+++ b/src/libra/common/hadoop/io/reader/sequence/RawReadReader.java
@@ -35,110 +35,286 @@ public class RawReadReader implements Closeable {
 
     private static final Log LOG = LogFactory.getLog(RawReadReader.class);
     
+    private static final int LINE_BUFFERS = 4;
+    
     private SampleFormat format;
     private LineReader in;
-    private Text buffer = new Text();
-    private int bufferConsumed;
-    private char delimiter;
+    private Text[] buffers = new Text[LINE_BUFFERS];
+    private int[] bufferConsumed = new int[LINE_BUFFERS];
+    private boolean eof = false;
     private boolean finished = false;
 
     public RawReadReader(SampleFormat format, InputStream in) {
         this.format = format;
         this.in = new LineReader(in);
-        this.bufferConsumed = 0;
+        for(int i=0;i<LINE_BUFFERS;i++) {
+            this.buffers[i] = new Text();
+            this.bufferConsumed[i] = 0;
+        }
+        this.eof = false;
         this.finished = false;
-        
-        _setDelimiter();
     }
     
     public RawReadReader(SampleFormat format, InputStream in, int bufferSize) {
         this.format = format;
         this.in = new LineReader(in, bufferSize);
-        this.bufferConsumed = 0;
+        for(int i=0;i<LINE_BUFFERS;i++) {
+            this.buffers[i] = new Text();
+            this.bufferConsumed[i] = 0;
+        }
+        this.eof = false;
         this.finished = false;
-        
-        _setDelimiter();
     }
     
     public RawReadReader(SampleFormat format, InputStream in, Configuration conf) throws IOException {
         this.format = format;
         this.in = new LineReader(in, conf);
-        this.bufferConsumed = 0;
+        for(int i=0;i<LINE_BUFFERS;i++) {
+            this.buffers[i] = new Text();
+            this.bufferConsumed[i] = 0;
+        }
+        this.eof = false;
         this.finished = false;
-        
-        _setDelimiter();
     }
 
     @Override
     public void close() throws IOException {
+        this.eof = true;
         this.finished = true;
         this.in.close();
     }
     
-    private void _setDelimiter() {
-        switch(this.format) {
-            case FASTA:
-                this.delimiter = Read.FASTA_READ_DESCRIPTION_IDENTIFIER;
-                break;
-            case FASTQ:
-                this.delimiter = Read.FASTQ_READ_DESCRIPTION_IDENTIFIER;
+    private void _shiftBuffer(int steps) {
+        if(steps <= 0) {
+            return;
+        }
+        
+        if(steps >= LINE_BUFFERS) {
+            for(int i=0;i<LINE_BUFFERS;i++) {
+                this.buffers[i].clear();
+                this.bufferConsumed[i] = 0;
+            }
+        } else {
+            for(int i=0;i<LINE_BUFFERS;i++) {
+                if(i+steps < LINE_BUFFERS) {
+                    Text temp = this.buffers[i];
+                    this.buffers[i] = this.buffers[i+steps];
+                    this.buffers[i+steps] = temp;
+                    this.buffers[i+steps].clear();
+                    this.bufferConsumed[i] = this.bufferConsumed[i+steps];
+                }
+            }
+            
+            for(int i=0;i<steps;i++) {
+                int idx = LINE_BUFFERS-i-1;
+                this.buffers[idx].clear();
+                this.bufferConsumed[idx] = 0;
+            }
+        }
+    }
+    
+    private int _countEmptyBuffer() {
+        int count = 0;
+        for(int i=0;i<LINE_BUFFERS;i++) {
+            int idx = LINE_BUFFERS-i-1;
+            if(this.bufferConsumed[idx] == 0) {
+                count++;
+            } else {
                 break;
+            }
         }
+        return count;
     }
     
-    private boolean _fillBuffer(boolean force) throws IOException {
+    private boolean _fillBuffer() throws IOException {
         // returns hasData
-        if(this.bufferConsumed == 0 || force) {
-            // fill buffer
-            this.bufferConsumed = this.in.readLine(this.buffer, Integer.MAX_VALUE, Integer.MAX_VALUE);
-            if(this.bufferConsumed <= 0) {
-                this.bufferConsumed = 0;
+        int emptyBuffers = _countEmptyBuffer();
+        if(this.eof) {
+            if(emptyBuffers == LINE_BUFFERS) {
                 return false;
             } else {
                 return true;
             }
+        }
+        
+        if(emptyBuffers > 0) {
+            // fill buffer
+            int filled = 0;
+            for(int i=0;i<emptyBuffers;i++) {
+                int idx = LINE_BUFFERS-emptyBuffers+i;
+                this.bufferConsumed[idx] = this.in.readLine(this.buffers[idx], Integer.MAX_VALUE, Integer.MAX_VALUE);
+                if(this.bufferConsumed[idx] <= 0) {
+                    this.buffers[idx].clear();
+                    this.bufferConsumed[idx] = 0;
+                    this.eof = true;
+                    break;
+                } else {
+                    filled++;
+                }
+            }
+            
+            if(LINE_BUFFERS - emptyBuffers + filled > 0) {
+                return true;
+            } else {
+                return false;
+            }
         } else {
             return true;
         }
     }
-
-    public long skipIncompleteRead() throws IOException {
+    
+    private long _skipIncompleteFASTARead() throws IOException {
         if(this.finished) {
             return 0;
         }
         
+        boolean hasBufferData = _fillBuffer();
+        if(!hasBufferData) {
+            //EOF
+            this.finished = true;
+            return 0;
+        }
+        
         long bytesConsumed = 0;
+        boolean headerFound = false;
+        while(hasBufferData) {
+            if(this.buffers[0].getLength() > 0 && this.buffers[0].charAt(0) == Read.FASTA_READ_DESCRIPTION_IDENTIFIER) {
+                headerFound = true;
+                break;
+            } else {
+                bytesConsumed += this.bufferConsumed[0];
+                // refill buffer
+                _shiftBuffer(1);
+                hasBufferData = _fillBuffer();
+            }
+        }
         
-        boolean hasBufferData = _fillBuffer(false);
+        if(!headerFound) {
+            //EOF
+            this.finished = true;
+        }
+        
+        return bytesConsumed;
+    }
+
+    private long _skipIncompleteFASTQRead() throws IOException {
+        if(this.finished) {
+            return 0;
+        }
+        
+        boolean hasBufferData = _fillBuffer();
         if(!hasBufferData) {
             //EOF
             this.finished = true;
-            return bytesConsumed;
+            return 0;
         }
         
+        long bytesConsumed = 0;
         boolean headerFound = false;
         while(hasBufferData) {
-            if(this.buffer.getLength() > 0 && this.buffer.charAt(0) == this.delimiter) {
+            int emptyBufferCount = _countEmptyBuffer();
+            if(this.buffers[0].getLength() > 0 && this.buffers[0].charAt(0) == Read.FASTQ_READ_DESCRIPTION_IDENTIFIER &&
+                    this.buffers[2].getLength() > 0 && this.buffers[2].charAt(0) == Read.FASTQ_READ_DESCRIPTION2_IDENTIFIER && 
+                    emptyBufferCount == 0) {
                 headerFound = true;
                 break;
             } else {
-                bytesConsumed += this.bufferConsumed;
+                bytesConsumed += this.bufferConsumed[0];
                 // refill buffer
-                hasBufferData = _fillBuffer(true);
+                _shiftBuffer(1);
+                hasBufferData = _fillBuffer();
             }
         }
         
         if(!headerFound) {
             //EOF
-            bytesConsumed += this.bufferConsumed;
             this.finished = true;
-            this.bufferConsumed = 0;
         }
         
         return bytesConsumed;
     }
     
-    public long readRead(Read read) throws IOException {
+    public long skipIncompleteRead() throws IOException {
+        switch(this.format) {
+            case FASTA:
+                return _skipIncompleteFASTARead();
+            case FASTQ:
+                return _skipIncompleteFASTQRead();
+            default:
+                throw new IOException("Unknown format");
+        }
+    }
+    
+    private void _printBuffer() {
+        for(int i=0;i<LINE_BUFFERS;i++) {
+            LOG.info(String.format("BUFFER[%d] = %s (%d)", i, this.buffers[i].toString(), this.bufferConsumed[i]));
+        }
+    }
+    
+    private long _readFASTARead(Read read) throws IOException {
+        read.clear();
+        
+        long bytesConsumed = 0;
+        bytesConsumed += skipIncompleteRead();
+        
+        if(this.finished) {
+            return bytesConsumed;
+        }
+        
+        // check buffer has a header
+        boolean hasBufferData = _fillBuffer();
+        if(!hasBufferData) {
+            //EOF
+            this.finished = true;
+            return bytesConsumed;
+        }
+        
+        if(this.buffers[0].getLength() > 0 && this.buffers[0].charAt(0) == Read.FASTA_READ_DESCRIPTION_IDENTIFIER) {
+            // GO!
+            // add header
+            List<String> lines = new ArrayList<String>();
+        
+            String lineStr = this.buffers[0].toString();
+            if(lineStr.trim().length() > 0) {
+                lines.add(lineStr);
+            }
+            
+            bytesConsumed += this.bufferConsumed[0];
+            _shiftBuffer(1);
+            hasBufferData = _fillBuffer();
+            
+            boolean nextHeaderFound = false;
+            while(hasBufferData) {
+                if(this.buffers[0].getLength() > 0 && this.buffers[0].charAt(0) == Read.FASTA_READ_DESCRIPTION_IDENTIFIER) {
+                    nextHeaderFound = true;
+                    break;
+                } else {
+                    lineStr = this.buffers[0].toString();
+                    if(lineStr.trim().length() > 0) {
+                        lines.add(lineStr);
+                    }
+
+                    bytesConsumed += this.bufferConsumed[0];
+                    // refill buffer
+                    _shiftBuffer(1);
+                    hasBufferData = _fillBuffer();
+                }
+            }
+            
+            if(!nextHeaderFound) {
+                //EOF
+                this.finished = true;
+            }
+            
+            read.parse(lines);
+        } else {
+            throw new IOException(String.format("Unknown data for FASTA read - %s", this.buffers[0].toString()));
+        }
+        
+        return bytesConsumed;
+    }
+    
+    private long _readFASTQRead(Read read) throws IOException {
         read.clear();
         
         long bytesConsumed = 0;
@@ -149,40 +325,50 @@ public long readRead(Read read) throws IOException {
         }
         
         // check buffer has a header
-        boolean hasBufferData = _fillBuffer(false);
+        boolean hasBufferData = _fillBuffer();
         if(!hasBufferData) {
             //EOF
             this.finished = true;
             return bytesConsumed;
         }
         
-        if(this.buffer.getLength() > 0 && this.buffer.charAt(0) == this.delimiter) {
+        int emptyBufferCount = _countEmptyBuffer();
+        if(this.buffers[0].getLength() > 0 && this.buffers[0].charAt(0) == Read.FASTQ_READ_DESCRIPTION_IDENTIFIER &&
+                this.buffers[2].getLength() > 0 && this.buffers[2].charAt(0) == Read.FASTQ_READ_DESCRIPTION2_IDENTIFIER &&
+                emptyBufferCount == 0) {
             // GO!
             // add header
             List<String> lines = new ArrayList<String>();
         
-            String lineStr = this.buffer.toString();
+            String lineStr = this.buffers[0].toString();
             if(lineStr.trim().length() > 0) {
                 lines.add(lineStr);
             }
             
-            bytesConsumed += this.bufferConsumed;
-            hasBufferData = _fillBuffer(true);
+            bytesConsumed += this.bufferConsumed[0];
+            _shiftBuffer(1);
+            hasBufferData = _fillBuffer();
             
             boolean nextHeaderFound = false;
             while(hasBufferData) {
-                if(this.buffer.getLength() > 0 && this.buffer.charAt(0) == this.delimiter) {
+                emptyBufferCount = _countEmptyBuffer();
+                //_printBuffer();
+                
+                if(this.buffers[0].getLength() > 0 && this.buffers[0].charAt(0) == Read.FASTQ_READ_DESCRIPTION_IDENTIFIER &&
+                        this.buffers[2].getLength() > 0 && this.buffers[2].charAt(0) == Read.FASTQ_READ_DESCRIPTION2_IDENTIFIER &&
+                        emptyBufferCount == 0) {
                     nextHeaderFound = true;
                     break;
                 } else {
-                    lineStr = this.buffer.toString();
+                    lineStr = this.buffers[0].toString();
                     if(lineStr.trim().length() > 0) {
                         lines.add(lineStr);
                     }
 
-                    bytesConsumed += this.bufferConsumed;
+                    bytesConsumed += this.bufferConsumed[0];
                     // refill buffer
-                    hasBufferData = _fillBuffer(true);
+                    _shiftBuffer(1);
+                    hasBufferData = _fillBuffer();
                 }
             }
             
@@ -193,9 +379,20 @@ public long readRead(Read read) throws IOException {
             
             read.parse(lines);
         } else {
-            throw new IOException(String.format("Unknown data - %s", this.buffer.toString()));
+            throw new IOException(String.format("Unknown data for FASTQ read - %s", this.buffers[0].toString()));
         }
         
         return bytesConsumed;
     }
+    
+    public long readRead(Read read) throws IOException {
+        switch(this.format) {
+            case FASTA:
+                return _readFASTARead(read);
+            case FASTQ:
+                return _readFASTQRead(read);
+            default:
+                throw new IOException("Unknown format");
+        }
+    }
 }