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/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
+ *
+ * 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 htsjdk.samtools.SAMUtils;
+import htsjdk.samtools.fastq.FastqRecord;
+
+import java.util.ArrayList;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class ReadLayoutConsumer {
+	private static Logger log = LoggerFactory.getLogger(ReadLayoutConsumer.class);
+	
+
+	private static final byte BYTECODE_SAMPLE = 0;
+	private static final byte BYTECODE_BARCODE = 1;
+	private static final byte BYTECODE_UMI = 2;
+	
+	
+	ArrayList<Byte> slotCodes = new ArrayList<Byte>();
+	ArrayList<Integer> slotIdx = new ArrayList<Integer>();
+	ArrayList<Set<Integer>> layoutIndicesToUseForSlots = new ArrayList<Set<Integer>>();
+	ReadLayout [] readLayouts;
+	String outPutLayout;
+	
+	/**
+	 * @param outPutLayout in short format
+	 * @param readLayouts all ordered layout (order is as the reads are read from files)
+	 */
+	public ReadLayoutConsumer(String outPutLayout, ReadLayout [] readLayouts){
+		this.outPutLayout = outPutLayout;
+		this.readLayouts = readLayouts;
+
+		Pattern sub = Pattern.compile("([BUS])(\\d+)");
+		Matcher subMatcher = sub.matcher("");
+
+		Pattern p = Pattern.compile("([BUS]\\d+)");
+		Matcher m = p.matcher(outPutLayout);
+		log.debug("ReadLayoutConsumer created with "+outPutLayout);
+		while(m.find()){
+			String _g = m.group();
+			log.debug(_g);
+			subMatcher.reset(_g);
+			subMatcher.matches();
+			String slotType = subMatcher.group(1);
+			Integer slotId = Integer.parseInt(subMatcher.group(2));
+
+			//save the slot code
+			byte bCode ;
+			if(slotType.equalsIgnoreCase("B"))
+				bCode = BYTECODE_BARCODE;
+			else if(slotType.equalsIgnoreCase("U"))
+				bCode = BYTECODE_UMI;
+			else 
+				bCode = BYTECODE_SAMPLE;
+
+			log.debug("slot type "+slotType+" => "+bCode);
+			log.debug("slot id => "+slotId);
+
+			slotCodes.add(bCode);
+
+			//save the slot id
+			slotIdx.add(slotId);
+
+			//identify the ReadLayout to use to extract this slot
+			Set<Integer> allPossibleLayoutIdxToUse = new TreeSet<Integer>();
+			for (int i = 0; i < readLayouts.length; i++) {
+				ReadLayout rl = readLayouts[i];
+
+				boolean canBeUsed = false;
+				switch (bCode) {
+				case BYTECODE_BARCODE:
+					canBeUsed = rl.containsBarcode() && rl.getBarcodeBlockUniqueIds().contains(slotId); 
+					break;
+				case BYTECODE_UMI:
+					canBeUsed = rl.containsUMI() && rl.getUMIBlockUniqueIds().contains(slotId);
+					break;
+				case BYTECODE_SAMPLE:
+					canBeUsed = rl.containsSampleSequence() && rl.getSampleBlockUniqueIds().contains(slotId);
+					break;
+				default:
+					throw new LayoutMalformedException("unknown block code in output layout :"+bCode, outPutLayout);
+				}
+
+				if(canBeUsed){
+					allPossibleLayoutIdxToUse.add(i);
+					log.debug("ReadLayout idx "+i+" can be used for lookup");
+
+				}
+			}
+			if(allPossibleLayoutIdxToUse.isEmpty())
+				throw new LayoutMalformedException("no read layout identified for block "+slotType+" with index "+slotIdx, this.outPutLayout);
+			layoutIndicesToUseForSlots.add(allPossibleLayoutIdxToUse);
+		}
+	}
+
+
+	/**
+	 * Assemble a read name by concatenating the output layout to the original read name.  
+	 * Concatenation is made by inserting a readNameDelimitor between each added slot 
+	 *  
+	 * 
+	 * @param reads the reads in order matching that of the {@link ReadLayout} array used 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 String assembleNewReadName(FastqRecord [] reads, boolean[] useReadSequenceForBarcodes, SampleMatch m){
+
+		String newname = reads[0].getReadName().split("\\s")[0];
+		if(newname.endsWith(FastqWriterLayout.readNameDelimitor))
+			newname = newname.substring(0, newname.length()-1);
+		
+		log.debug("assembling read name with pattern "+this.outPutLayout);
+		for (int i = 0; i < slotCodes.size(); i++) {
+			byte slotTypeCode = slotCodes.get(i);
+			int slotIdx = this.slotIdx.get(i); 
+			log.debug("assembling read name adding slot code "+slotTypeCode+" with id "+slotIdx);
+			/*
+			 * when a slot can be obtained from different reads (e.g. redundant barcode), keep the one with best overall quality
+			 */
+			String subseq = null;
+			int bestQual = 0;
+			if(!useReadSequenceForBarcodes[slotIdx-1] && slotTypeCode == BYTECODE_BARCODE){
+				// we init the subseq with the matched barcode directly
+				subseq = m.getBarcodeMatches().get(slotIdx).barcode;
+			}else{
+				for(int rlIdx : layoutIndicesToUseForSlots.get(i)){
+
+					ReadLayout rl = readLayouts[rlIdx];
+					FastqRecord readForLayout = reads[rlIdx];
+
+					String _subseq = null;
+					String _subqual = null;
+					switch (slotTypeCode) {
+					case BYTECODE_BARCODE:
+						_subseq  = rl.extractBarcode(readForLayout.getReadString(), slotIdx);
+						_subqual = rl.extractBarcode(readForLayout.getBaseQualityString(), slotIdx);
+						break;
+					case BYTECODE_UMI:
+						_subseq = rl.extractUMI(readForLayout.getReadString(), slotIdx);
+						_subqual = rl.extractUMI(readForLayout.getBaseQualityString(), slotIdx);
+						break;
+					default:
+						_subseq = rl.extractSample(readForLayout.getReadString(), slotIdx);
+						_subqual = rl.extractSample(readForLayout.getBaseQualityString(), slotIdx);
+						break;
+					}
+					int _qualsum = overallQuality( SAMUtils.fastqToPhred(_subqual) );
+					if(subseq == null || _qualsum > bestQual){
+						subseq = _subseq;
+						bestQual = _qualsum;
+					}
+				}
+			}
+			//concatenate to the growing name
+			newname += FastqWriterLayout.readNameDelimitor + subseq;
+			log.debug("header is now : "+newname);
+		}
+
+		return newname;
+	}
+
+	/**
+	 * Assemble a FastqRecord using original read name and quality header. 
+	 * The read sequence (and associated quality string) are assembled according to the 
+	 * output layout given to this consumer 
+	 * 
+	 * @param reads the reads in order matching that of the {@link ReadLayout} array used at construction
+	 * @return
+	 */
+	public FastqRecord assembleNewRead(FastqRecord [] reads){
+
+		String newseq = "";
+		String newqual = "";
+
+		log.debug("#####  assembling read according to layout "+this.outPutLayout);
+		for (int i = 0; i < slotCodes.size(); i++) {
+			byte slotTypeCode = slotCodes.get(i);
+			int slotIdx = this.slotIdx.get(i); 
+
+			log.debug("gettign info for slot code "+slotTypeCode+" with idx "+slotIdx);
+			/*
+			 * when a slot can be obtained from different reads (e.g. redundant barcode), keep the one with best overall quality
+			 */
+			String subseq = null;
+			String subqual = null;
+			int bestQual = 0;
+			
+			for(int rlIdx : layoutIndicesToUseForSlots.get(i)){
+				ReadLayout rl = readLayouts[rlIdx];
+				FastqRecord readForLayout = reads[rlIdx];
+				String _subseq, _subqual = null;
+				switch (slotTypeCode) {
+				case BYTECODE_BARCODE:
+					_subseq  = rl.extractBarcode(readForLayout.getReadString(), slotIdx);
+					_subqual = rl.extractBarcode(readForLayout.getBaseQualityString(), slotIdx);
+					break;
+				case BYTECODE_UMI:
+					_subseq = rl.extractUMI(readForLayout.getReadString(), slotIdx);
+					_subqual = rl.extractUMI(readForLayout.getBaseQualityString(), slotIdx);
+					break;
+				default:
+					_subseq = rl.extractSample(readForLayout.getReadString(), slotIdx);
+					_subqual = rl.extractSample(readForLayout.getBaseQualityString(), slotIdx);
+					break;
+				}
+				int _qualsum = overallQuality( SAMUtils.fastqToPhred(_subqual) );
+				
+				if(subseq == null || _qualsum > bestQual){
+					subseq = _subseq;
+					subqual = _subqual;
+					bestQual = _qualsum;
+				}
+			}
+			
+			//concatenate to the growing newseq/newqual
+			newseq+=subseq;
+			newqual+=subqual;
+			
+		}
+		//log.debug(newseq);
+		//log.debug(newqual);
+		//we borrow read name and qual header from first read, which must always be here
+		return new FastqRecord(reads[0].getReadName().split("\\s")[0], newseq, reads[0].getBaseQualityHeader(), newqual);
+	}
+
+	private int overallQuality(byte [] qualScores) {
+		int s = 0;
+		for (byte b : qualScores) {
+			s+= b;
+		}
+		return s;
+	}
+
+}
+
+

src/main/java/org/embl/gbcs/je/SampleMatch.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.Map;
+
+/** Utility class to hang onto data about the best match for a given barcode */
+public class SampleMatch {
+	
+	
+		/**
+		 * The identified sample name or null 
+		 * 
+		 */
+		protected String sample;
+	
+		/**
+		 * The {@link BarcodeMatch} or null for each barcode slot
+		 * A {@link BarcodeMatch} is always present if the sample has been identified
+		 */
+		protected Map<Integer, BarcodeMatch> barcodeMatches;
+		
+		
+		public SampleMatch(String sample, Map<Integer, BarcodeMatch> barcodeMatches){
+			this.sample= sample;
+			this.barcodeMatches = barcodeMatches;
+		}
+
+
+		/**
+		 * @return the sample
+		 */
+		public String getSample() {
+			return sample;
+		}
+
+
+		/**
+		 * @return the barcodeMatches
+		 */
+		public Map<Integer, BarcodeMatch> getBarcodeMatches() {
+			return barcodeMatches;
+		}
+
+
+		/**
+		 * @param sample the sample to set
+		 */
+		public void setSample(String sample) {
+			this.sample = sample;
+		}
+
+
+		/**
+		 * @param barcodeMatches the barcodeMatches to set
+		 */
+		public void setBarcodeMatches(Map<Integer, BarcodeMatch> barcodeMatches) {
+			this.barcodeMatches = barcodeMatches;
+		}
+		
+	
+}

src/main/java/org/embl/gbcs/je/demultiplexer/BarcodeFileSimpleToGeneralFormatConverter.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.demultiplexer;
+
+import htsjdk.samtools.fastq.FastqReader;
+import htsjdk.samtools.fastq.FastqRecord;
+
+import java.io.File;