added all functionality, needs in depth tsting now

lib/README.txt

 #jars found in this folder are artifact that are not found in maven central, you can then puch them in your local maven repo with the following commands:
 
-#ADAPT fpath to YOUR Je/lib
-LIBPATH="/Users/girardot/Work/eclipse_ws/Je/lib/"
+#ADAPT path to YOUR Je/lib
+LIBPATH="/Users/girardot/git/Je/lib/"
 cd ~/.m2 
-mvn install:install-file -DgroupId=net.sf -DartifactId=htsjdk -Dversion=1.140custom -Dfile=$LIBPATH/custom-picard/htsjdk-1.140.jar -Dpackaging=jar -DgeneratePom=true 
-mvn install:install-file -DgroupId=net.sf -DartifactId=picard -Dversion=1.140custom -Dfile=$LIBPATH/custom-picard/picard.jar -Dpackaging=jar -DgeneratePom=true
+mvn install:install-file -DgroupId=org.broadinstitute -DartifactId=picard -Dversion=2.9.4 -Dfile=$LIBPATH/picard_2.9.4.jar -Dpackaging=jar -DgeneratePom=true
 
 # Uncomment to ADD GBCS artifacts if needed (ie if you don t have access to these repos)
 # IF you are at embl, you rather want to checkout the relevant projects and build them locally

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>Je</groupId>
 	<artifactId>Je</artifactId>
-	<version>1.1</version>
+	<version>2.0.beta</version>
 	<name>Je</name>
 	<description>Je provides command line utilities to deal with barcoded FASTQ files with or without Unique Molecular Index (UMI)</description>
 
@@ -233,34 +233,9 @@
 		<dependency>
 			<groupId>org.embl.cg.utilitytools</groupId>
 			<artifactId>ut_utils</artifactId>
-			<version>1.0</version>
-		</dependency>
-		
-		<!-- <dependency> -->
-		<!-- <groupId>net.sf</groupId> -->
-		<!-- <artifactId>picard</artifactId> -->
-		<!-- <version>1.140</version> -->
-		<!-- </dependency> -->
-		<!-- <dependency> -->
-		<!-- <groupId>net.sf</groupId> -->
-		<!-- <artifactId>htsjdk</artifactId> -->
-		<!-- <version>1.140</version> -->
-		<!-- </dependency> -->
-
-		<dependency>
-			<groupId>net.sf</groupId>
-			<artifactId>picard</artifactId>
-			<version>1.140custom</version>
-
+			<version>1.0.1</version>
 		</dependency>
-		<dependency>
-			<groupId>net.sf</groupId>
-			<artifactId>htsjdk</artifactId>
-			<version>1.140custom</version>
-
-		</dependency>
-
-
+	
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-api</artifactId>
@@ -291,6 +266,11 @@
 			<version>4.11</version>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.broadinstitute</groupId>
+			<artifactId>picard</artifactId>
+			<version>2.9.4</version>
+		</dependency>
 	</dependencies>
 
 

src/main/java/org/embl/gbcs/je/jemultiplexer/ApplicationConfiguration.java → src/main/java/org/embl/gbcs/je/ApplicationConfiguration.java

@@ -21,7 +21,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.embl.gbcs.je.jemultiplexer;
+package org.embl.gbcs.je;
 
 import java.io.IOException;
 import java.io.InputStream;

src/main/java/org/embl/gbcs/je/jemultiplexer/BarcodeMatch.java → src/main/java/org/embl/gbcs/je/BarcodeMatch.java

@@ -21,13 +21,15 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.embl.gbcs.je.jemultiplexer;
+package org.embl.gbcs.je;
 
 /** Utility class to hang onto data about the best match for a given barcode */
 public class BarcodeMatch {
 	
+	
+	
 		/**
-		 * indicates if a barcode match has been found, in which case 'barcode' is not null 
+		 * indicates if this barcode match fullfils the thresholds for barcode matching  
 		 */
 		public boolean matched;
 		
@@ -35,6 +37,12 @@ public class BarcodeMatch {
 		 * sequence of the matched barcode 
 		 */
 		public String barcode;
+	
+		/**
+		 * sequence extracted from read   
+		 */
+		public String readSequence;
+	
 		
 		/**
 		 * number of mismatches with 'barcode'
@@ -48,8 +56,9 @@ public class BarcodeMatch {
 		
 		public String toString(){
 			if(matched)
-				return "matched :"+ barcode+" [MM="+mismatches+", MMD="+mismatchesToSecondBest+"]";
-			return "no match";
+				return "Match for "+readSequence+ " read sequence : barcode "+ barcode+" identified with [MM="+mismatches+", MMD="+mismatchesToSecondBest+"]";
+			else
+				return "No Match for "+readSequence+ " read sequence (best barcode is "+ barcode+" identified with [MM="+mismatches+", MMD="+mismatchesToSecondBest+"])";
 		}
 	
 }

src/main/java/org/embl/gbcs/je/FastqWriterLayout.java

+/*
+ * The MIT License
+ *
+ * Copyright (c) 2009 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+package org.embl.gbcs.je;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.commons.lang3.StringUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import picard.util.MathUtil;
+import htsjdk.samtools.fastq.FastqRecord;
+
+/**
+ * 
+ * Describes how and what to write in FASTQ output files when demultiplexing input FASTQ files
+ * More precisely, it describes the output file layout(s) using the slots defined in read layouts e.g. '<BARCODE1><UMI1><UMI2>' or '<SAMPLE1>'  
+ * Each FastqWriterLayout needs two of these descriptors : 
+ *   1. One describing how to write the read sequence e.g. '<SAMPLE1>' (only writes the sample sequence) or '<BARCODE1><SAMPLE1>' to also 
+ *      keep the barcode in the output read sequence (and qualities)
+ *   2. A second one describing how to write the read name (header) e.g. '<BARCODE1><UMI1><UMI2>' to add the barcode and two extracted UMIs 
+ *      in the final read name, in addition to the original read name (ie header up to the space). Here each written slot is separated with ':' by default
+ *      
+ * 
+ * Note that a short layout format can also be used like 'B1', 'U2', 'S1'' instead of '<BARCODE1>' , '<UMI2>' and '<SAMPLE1>' ; respectively. 
+ * For example, 'B1U1U2' is the same as '<BARCODE1><UMI1><UMI2>'. 
+ * 
+ *  Technically speaking, the short layout format is the only one used.  
+ * 
+ * @author girardot
+ *
+ */
+public class FastqWriterLayout {
+
+	private static Logger log = LoggerFactory.getLogger(FastqWriterLayout.class);
+	
+	private static final String LONG_LAYOUT_REGEX = "^(<?(BARCODE|UMI|SAMPLE)\\d+>?)+$";
+	private static final String SHORT_LAYOUT_REGEX = "^([BUS]\\d+)+$";
+	
+	
+	
+	/**
+	 * char to use to delineate slots in read name ; if needed
+	 */
+	protected static String readNameDelimitor = ":";
+	
+	
+	
+	/**
+	 * Layout for writing the read sequence ; in short format 
+	 */
+	protected String readSequenceLayout;
+	
+	/**
+	 * Consumer associated with the readSequenceLayout
+	 */
+	protected ReadLayoutConsumer sequenceConsumer;
+	
+	/**
+	 * Layout for writing the read name ; in short format 
+	 */
+	protected String readNameLayout;
+	
+	/**
+	 * Consumer associated with the readNameLayout
+	 */
+	protected ReadLayoutConsumer readNameConsumer ;
+	
+	
+	
+	/**
+	 * All the {@link ReadLayout} defined in the demultiplexing ; used to find how to extract needed information  
+	 */
+	protected ReadLayout [] readLayouts;
+	
+	/**
+	 * @param readSequenceLayout
+	 * @param readNameLayout can be null when the read name should be reused unmodified
+	 * @param readLayouts
+	 */
+	public FastqWriterLayout(final String readSequenceLayout, final String readNameLayout, final ReadLayout [] readLayouts) {
+		
+		this.readNameLayout = (StringUtils.isBlank(readNameLayout) ? null : convertToShortLayout(readNameLayout));
+		this.readSequenceLayout = convertToShortLayout(readSequenceLayout);
+		this.readLayouts = readLayouts;
+		init(); //build all maps for easy lookup
+	}
+	
+	/**
+	 * @param readSequenceLayout
+	 * @param readNameLayout can be null when the read name should be reused unmodified
+	 * @param readLayout
+	 */
+	public FastqWriterLayout(final String readSequenceLayout, final String readNameLayout, final ReadLayout readLayout) {
+		this(readSequenceLayout, readNameLayout, new ReadLayout[]{ readLayout });
+	}
+
+	
+	/**
+	 * @param layout
+	 * @return
+	 */
+	private String convertToShortLayout(final String layout) {
+		log.debug("given layout : "+layout);
+		if(StringUtils.isBlank(layout))
+			return layout;
+		String shortLayout = layout;
+		if(!Pattern.matches(SHORT_LAYOUT_REGEX, layout)){
+			if(!Pattern.matches(LONG_LAYOUT_REGEX, layout))
+				throw new LayoutMalformedException("FASTQ Output Layout does not match expected short ("+SHORT_LAYOUT_REGEX+") nor long ("+LONG_LAYOUT_REGEX+") formats", layout);
+			
+			//convert to short
+			shortLayout = shortLayout.replaceAll("<", "");
+			shortLayout = shortLayout.replaceAll(">", "");
+			shortLayout = shortLayout.replaceAll("ARCODE", "");
+			shortLayout = shortLayout.replaceAll("MI", "");
+			shortLayout = shortLayout.replaceAll("AMPLE", "");
+		}
+		log.debug("short layout : "+shortLayout);
+		return shortLayout;
+		
+	}
+
+
+	/**
+	 * Assemble the {@link FastqRecord} that should be written in the output file according to the layout(s)
+	 * @param reads the {@link FastqRecord} from the input fastq files in the order matching the {@link ReadLayout} given at construction 
+	 * @param useReadSequenceForBarcodes dictates what to write in the read header layouts of the {@link FastqWriterLayout} for each BARCODE.
+	 * When false, the matched barcode is used. When true, the exact read sequence extracted from the barcode slot is written
+	 * @param m a {@link SampleMatch} holding all the barcode matches
+	 * @return
+	 */
+	public FastqRecord assembleRecord( FastqRecord[] reads, boolean[] useReadSequenceForBarcodes, SampleMatch m ){
+		
+		FastqRecord rec = sequenceConsumer.assembleNewRead(reads);
+		String name = rec.getReadName(); 
+		if(readNameConsumer != null) 
+			name = readNameConsumer.assembleNewReadName(reads, useReadSequenceForBarcodes, m);
+		
+		FastqRecord ass = new FastqRecord(name, rec.getReadString(), rec.getBaseQualityHeader(), rec.getBaseQualityString());
+		log.debug("Assembled read for output using layout [NameLayout="+this.readNameLayout+" ; SequenceLayout="+this.readSequenceLayout+"] => \n"+ass.toFastQString());
+		return ass;
+	}
+	
+	/**
+	 * Convenient wrapper for single end configuration
+	 * @param read the {@link FastqRecord} from the input fastq file
+	 * @param useReadSequenceForBarcodes dictates what to write in the read header layouts of the {@link FastqWriterLayout} for each BARCODE.
+	 * When false, the matched barcode is used. When true, the exact read sequence extracted from the barcode slot is written
+	 * @param m a {@link SampleMatch} holdign all the barcode matches  
+	 * @return
+	 */
+	public FastqRecord assembleRecord( FastqRecord read, boolean[] useReadSequenceForBarcodes, SampleMatch m ){
+		return assembleRecord(new FastqRecord[]{read}, useReadSequenceForBarcodes, m);
+	}
+	
+	
+	
+	/**
+	 * Checks that this layout can be produced from a list of {@link ReadLayout}
+	 * @param readLayouts
+	 * @return
+	 */
+	protected void init(){
+		
+		
+		/*
+		 * Process (short format) layout for easy output assembly at FASTQ writing time
+		 */
+		
+		// do for read seq
+		if(!Pattern.matches(SHORT_LAYOUT_REGEX, this.readSequenceLayout)){
+			throw new LayoutMalformedException("FASTQ Output Layout for read sequence does not match expected short format (regex is :"+SHORT_LAYOUT_REGEX+")", this.readSequenceLayout);
+		}
+		sequenceConsumer = new ReadLayoutConsumer(this.readSequenceLayout, this.readLayouts);
+
+		// do for read name if not null
+		if( this.readNameLayout != null){
+			if(!Pattern.matches(SHORT_LAYOUT_REGEX, this.readNameLayout)){
+				throw new LayoutMalformedException("FASTQ Output Layout for read name does not match expected short format (regex is :"+SHORT_LAYOUT_REGEX+")", this.readNameLayout);
+			}
+			readNameConsumer = new ReadLayoutConsumer(this.readNameLayout, this.readLayouts);
+		}
+	}
+	
+	
+	/**
+	 * @param reads
+	 * @param readLayouts
+	 * @return
+	 */
+	public static Map<Integer, List<FastqRecord>> extractBarcodeSlots(FastqRecord[] reads, ReadLayout[] readLayouts) {
+		Map<Integer, List<FastqRecord>> m = new HashMap<Integer, List<FastqRecord>>();
+		
+		/*
+		 * for each read layout
+		 */
+		for (int i = 0; i < readLayouts.length; i++) {
+			//find those with BARCODE slot(s)
+			if(readLayouts[i].containsBarcode()){
+				//extract the BARCODE subsequence
+				String [] sequences = readLayouts[i].extractBarcodes(reads[i].getReadString());
+				//and the corresponding quality strings
+				String [] qualities = readLayouts[i].extractBarcodes(reads[i].getBaseQualityString());
+				//and the BARCODE idx corresponding to them
+				List<Integer> barcodeBlockIds = readLayouts[i].getOrderedBarcodeBlockUniqueIds();
+				//save each subsequence/quality as a FastqRecord in the list corresponding to the BARCODE idx
+				for (int j = 0; j < barcodeBlockIds.size(); j++) {
+					int blockId = barcodeBlockIds.get(j);
+					if(!m.containsKey(blockId))
+						m.put(blockId, new ArrayList<FastqRecord>());
+					
+					FastqRecord fr = new FastqRecord(null, sequences[j], null, qualities[j]);
+					log.debug("Extracted Barcode : "+fr.toFastQString());
+					m.get(blockId).add(
+							fr
+							);
+				}
+			}
+		}
+		return m;
+	}
+
+
+	/**
+	 * @return the readNameDelimitor
+	 */
+	public String getReadNameDelimitor() {
+		return readNameDelimitor;
+	}
+
+
+	/**
+	 * @param readNameDelimitor the readNameDelimitor to set
+	 */
+	public void setReadNameDelimitor(String readNameDelimitor) {
+		this.readNameDelimitor = readNameDelimitor;
+	}
+
+	/**
+	 * @return the readSequenceLayout in short format
+	 */
+	public String getReadSequenceLayout() {
+		return readSequenceLayout;
+	}
+
+	/**
+	 * @return the readNameLayout in short format
+	 */
+	public String getReadNameLayout() {
+		return readNameLayout;
+	}
+
+
+	
+}

src/main/java/org/embl/gbcs/je/Je.java

@@ -26,7 +26,9 @@ package org.embl.gbcs.je;
 import java.util.Set;
 import java.util.TreeSet;
 
+import org.embl.cg.utilitytools.utils.ExceptionUtil;
 import org.embl.cg.utilitytools.utils.StringUtil;
+import org.embl.gbcs.je.demultiplexer.Jedemultiplex;
 import org.embl.gbcs.je.jeclipper.Jeclipper;
 import org.embl.gbcs.je.jedropseq.Jedropseq;
 import org.embl.gbcs.je.jeduplicates.MarkDuplicatesWithMolecularCode;
@@ -48,6 +50,7 @@ public class Je  {
 	private static Logger log = LoggerFactory.getLogger(Je.class);
 
 	
+	public static final String COMMAND_DEMULTIPLEX = "debarcode"; 
 	public static final String COMMAND_DROPSEQ = "dropseq"; 
 	public static final String COMMAND_CLIP = "clip"; 
 	public static final String COMMAND_DUPES = "markdupes";
@@ -62,6 +65,7 @@ public class Je  {
 		ALLOWED_COMMANDS.add(COMMAND_MULTIPLEX);
 		ALLOWED_COMMANDS.add(COMMAND_MULTIPLEX_ILLUMINA);
 		ALLOWED_COMMANDS.add(COMMAND_DROPSEQ);
+		ALLOWED_COMMANDS.add(COMMAND_DEMULTIPLEX);
 		
 	}
 	
@@ -90,49 +94,57 @@ public class Je  {
 			System.exit(0); 
 		}
 		else if(!ALLOWED_COMMANDS.contains(option.toLowerCase())){
-			System.err.println("Unknown command name : "+option);
-			System.err.println(getUsage());
+			System.err.println("Unknown command name : "+option+" ; please check help with -h");
+			//System.err.println(getUsage());
 			System.exit(1); //error
 		}
 		
 		/*
 		 * looks good , we delegate to proper implementation
 		 */
-		String [] argv = {"-h"}; // init to get help
-		if(args.length > 1){
-			argv = StringUtil.subArray(args, 1, args.length-1);
-		}
-		if(option.equalsIgnoreCase(COMMAND_CLIP)){
-			new Jeclipper().instanceMainWithExit(argv); 
-		}
-		else if(option.equalsIgnoreCase(COMMAND_MULTIPLEX)){
-			new Jemultiplexer().instanceMainWithExit(argv);
-		}
-		else if(option.equalsIgnoreCase(COMMAND_MULTIPLEX_ILLUMINA)){
-			new JemultiplexerIllumina().instanceMainWithExit(argv);
-		}
-		else if(option.equalsIgnoreCase(COMMAND_DUPES)){
-			new MarkDuplicatesWithMolecularCode().instanceMainWithExit(argv);
-		}
-		else if(option.equalsIgnoreCase(COMMAND_DROPSEQ)){
-			new Jedropseq().instanceMainWithExit(argv);
-		}
-		else{
-			System.err.println(
-					"FATAL : We just reached a supposedly unreachable part of the code. Please report this bug to Je developpers indicating the options you used i.e. : \n "+
-					StringUtil.mergeArray(args, " ")
-					);
+		try{
+			String [] argv = {"-h"}; // init to get help
+			if(args.length > 1){
+				argv = StringUtil.subArray(args, 1, args.length-1);
+			}
+			if(option.equalsIgnoreCase(COMMAND_CLIP)){
+				new Jeclipper().instanceMainWithExit(argv); 
+			}
+			else if(option.equalsIgnoreCase(COMMAND_DEMULTIPLEX)){
+				new Jedemultiplex().instanceMainWithExit(argv);
+			}
+			else if(option.equalsIgnoreCase(COMMAND_MULTIPLEX)){
+				new Jemultiplexer().instanceMainWithExit(argv);
+			}
+			else if(option.equalsIgnoreCase(COMMAND_MULTIPLEX_ILLUMINA)){
+				new JemultiplexerIllumina().instanceMainWithExit(argv);
+			}
+			else if(option.equalsIgnoreCase(COMMAND_DUPES)){
+				new MarkDuplicatesWithMolecularCode().instanceMainWithExit(argv);
+			}
+			else if(option.equalsIgnoreCase(COMMAND_DROPSEQ)){
+				new Jedropseq().instanceMainWithExit(argv);
+			}
+			else{
+				System.err.println(
+						"FATAL : We just reached a supposedly unreachable part of the code. Please report this bug to Je developpers indicating the options you used i.e. : \n "+
+								StringUtil.mergeArray(args, " ")
+						);
+				System.exit(1); //error
+			}
+		} catch(Exception e){
+			log.error(ExceptionUtil.getStackTrace(e));
 			System.exit(1); //error
 		}
-		
 	}
 
 	protected static String getUsage(){
 		return "Usage:   je <command> [options] \n\n"+
 				"with command in : \n"
 				+"\t "+COMMAND_CLIP+"      \t\t clips molecular barcodes from fastq sequence and places them in read name headers for further use in 'dupes' module\n"
-				+"\t "+COMMAND_MULTIPLEX+" \t\t demultiplex fastq file(s), with optional handling of molecular barcodes for further use in 'dupes' module\n"
-				+"\t "+COMMAND_MULTIPLEX_ILLUMINA+" \t demultiplex fastq file(s) using Illumina Index files, with optional handling of molecular barcodes for further use in 'dupes' module\n"
+				+"\t "+COMMAND_DEMULTIPLEX+" \t\t demultiplexes fastq file(s), with optional handling of molecular barcodes for further use in 'dupes' module\n"
+				+"\t "+COMMAND_MULTIPLEX+" \t\t demultiplexes fastq file(s) with Je 1.x implementation, with optional handling of molecular barcodes for further use in 'dupes' module\n"
+				+"\t "+COMMAND_MULTIPLEX_ILLUMINA+" \t demultiplexes fastq file(s) using Illumina Index files with Je 1.x implementation, with optional handling of molecular barcodes for further use in 'dupes' module\n"
 				+"\t "+COMMAND_DUPES+"     \t\t removes read duplicates based on molecular barcodes found in read name headers (as produced by clip or plex)\n"
 				+"\t "+COMMAND_DROPSEQ+"    \t\t clips cell barcode and UMI from read 1 and adds them to header of read 2. This command is for processing drop-seq results.\n"
 				+"\n"

src/main/java/org/embl/gbcs/je/JeUtils.java

@@ -23,6 +23,9 @@
  */
 package org.embl.gbcs.je;
 
+import java.util.Set;
+import java.util.TreeSet;
+
 import com.developpez.adiguba.shell.ProcessConsumer;
 
 public class JeUtils {
@@ -61,6 +64,19 @@ public class JeUtils {
          
 		
 	}
+
+	public static int barcodeSlotCount(ReadLayout[] readLayouts) {
+		
+		return barcodeBlockUniqueIdSet(readLayouts).size();
+	}
+	
+	public static Set<Integer> barcodeBlockUniqueIdSet(ReadLayout[] readLayouts) {
+		Set<Integer> allIds = new TreeSet<Integer>();
+		for (ReadLayout rl : readLayouts) {
+			allIds.addAll(rl.getBarcodeBlockUniqueIds());
+		}
+		return allIds;
+	}
 	
 	
 	

src/main/java/org/embl/gbcs/je/jemultiplexer/JemultiplexerFastqWriterFactory.java → src/main/java/org/embl/gbcs/je/JemultiplexerFastqWriterFactory.java

@@ -21,7 +21,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.embl.gbcs.je.jemultiplexer;
+package org.embl.gbcs.je;
 
 import htsjdk.samtools.Defaults;
 import htsjdk.samtools.fastq.AsyncFastqWriter;
@@ -37,7 +37,7 @@ import java.util.zip.GZIPOutputStream;
 
 public class JemultiplexerFastqWriterFactory {
 
-	boolean useAsyncIo = Defaults.USE_ASYNC_IO;
+	boolean useAsyncIo = Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS;
 	
 
 	/** Sets whether or not to use async io (i.e. a dedicated thread per writer. */

src/main/java/org/embl/gbcs/je/ReadLayoutMalformedException.java → src/main/java/org/embl/gbcs/je/LayoutMalformedException.java

@@ -23,14 +23,14 @@
  */
 package org.embl.gbcs.je;
 
-public class ReadLayoutMalformedException extends Jexception {
+public class LayoutMalformedException extends Jexception {
 
 	/**
 	 * 
 	 */
 	private static final long serialVersionUID = -4024288961353288534L;
 
-	public ReadLayoutMalformedException(String message, String layout) {
+	public LayoutMalformedException(String message, String layout) {
 		super(message+"\n Layout was : "+layout);
 	}
 

src/main/java/org/embl/gbcs/je/ReadLayoutConsumer.java

+/*
+ * The MIT License
+ *
+ * Copyright (c) 2009 The Broad Institute