merge conflicts resolution

.gitignore

@@ -5,3 +5,4 @@ target/
 .DS_Store
 ._*
 embl.properties
+test.properties

.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>Je</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

.settings/org.eclipse.core.resources.prefs

+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
+encoding//src/test/resources=UTF-8
+encoding/<project>=UTF-8

.settings/org.eclipse.jdt.core.prefs

+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5
+org.eclipse.jdt.core.compiler.compliance=1.5
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.5

.settings/org.eclipse.jdt.ui.prefs

+eclipse.preferences.version=1
+org.eclipse.jdt.ui.javadoc=false
+org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8" standalone\="no"?><templates><template autoinsert\="true" context\="gettercomment_context" deleted\="false" description\="Comment for getter method" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.gettercomment" name\="gettercomment">/**\n * @return the ${bare_field_name}\n */</template><template autoinsert\="true" context\="settercomment_context" deleted\="false" description\="Comment for setter method" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.settercomment" name\="settercomment">/**\n * @param ${param} the ${bare_field_name} to set\n */</template><template autoinsert\="true" context\="constructorcomment_context" deleted\="false" description\="Comment for created constructors" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.constructorcomment" name\="constructorcomment">/**\n * ${tags}\n */</template><template autoinsert\="true" context\="filecomment_context" deleted\="false" description\="Comment for created Java files" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.filecomment" name\="filecomment">/**\n * \n */</template><template autoinsert\="true" context\="typecomment_context" deleted\="false" description\="Comment for created types" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.typecomment" name\="typecomment">/**\n * @author ${user}\n *\n * ${tags}\n */</template><template autoinsert\="true" context\="fieldcomment_context" deleted\="false" description\="Comment for fields" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.fieldcomment" name\="fieldcomment">/**\n * \n */</template><template autoinsert\="true" context\="methodcomment_context" deleted\="false" description\="Comment for non-overriding methods" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.methodcomment" name\="methodcomment">/**\n * ${tags}\n */</template><template autoinsert\="true" context\="overridecomment_context" deleted\="false" description\="Comment for overriding methods" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.overridecomment" name\="overridecomment">/* (non-Javadoc)\n * ${see_to_overridden}\n */</template><template autoinsert\="true" context\="delegatecomment_context" deleted\="false" description\="Comment for delegate methods" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.delegatecomment" name\="delegatecomment">/**\n * ${tags}\n * ${see_to_target}\n */</template><template autoinsert\="false" context\="newtype_context" deleted\="false" description\="Newly created files" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.newtype" name\="newtype">/*\n * The MIT License\n *\n * Copyright (c) 2009 The Broad Institute\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the "Software"), to deal\n * in the Software without restriction, including without limitation the rights\n * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n * copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions\:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n * THE SOFTWARE.\n */\n${filecomment}\n${package_declaration}\n\n${typecomment}\n${type_declaration}</template><template autoinsert\="true" context\="classbody_context" deleted\="false" description\="Code in new class type bodies" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.classbody" name\="classbody">\n</template><template autoinsert\="true" context\="interfacebody_context" deleted\="false" description\="Code in new interface type bodies" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.interfacebody" name\="interfacebody">\n</template><template autoinsert\="true" context\="enumbody_context" deleted\="false" description\="Code in new enum type bodies" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.enumbody" name\="enumbody">\n</template><template autoinsert\="true" context\="annotationbody_context" deleted\="false" description\="Code in new annotation type bodies" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.annotationbody" name\="annotationbody">\n</template><template autoinsert\="true" context\="catchblock_context" deleted\="false" description\="Code in new catch blocks" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.catchblock" name\="catchblock">// ${todo} Auto-generated catch block\n${exception_var}.printStackTrace();</template><template autoinsert\="true" context\="methodbody_context" deleted\="false" description\="Code in created method stubs" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.methodbody" name\="methodbody">// ${todo} Auto-generated method stub\n${body_statement}</template><template autoinsert\="true" context\="constructorbody_context" deleted\="false" description\="Code in created constructor stubs" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.constructorbody" name\="constructorbody">${body_statement}\n// ${todo} Auto-generated constructor stub</template><template autoinsert\="true" context\="getterbody_context" deleted\="false" description\="Code in created getters" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.getterbody" name\="getterbody">return ${field};</template><template autoinsert\="true" context\="setterbody_context" deleted\="false" description\="Code in created setters" enabled\="true" id\="org.eclipse.jdt.ui.text.codetemplates.setterbody" name\="setterbody">${field} \= ${param};</template></templates>

.settings/org.eclipse.m2e.core.prefs

+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

README.md

@@ -11,24 +11,40 @@ Additional documentation and support can be found at http://gbcs.embl.de/je
 
 ## The Je tool suite
 
-Je currently offers 4 tools:
+Je currently offers the following tools:
+
+
+* **je debarcode** 
+     
+     demultiplexes multi-samples fastq files using user-defined input *read-layouts* and write output files following user-defined *output-layouts*.
+     Replaces both **demultiplex-illu** and **demultiplex** since version 2.0.
+  
+* **je dropseq**
+     
+     to process drop-seq results: clips cell barcode and UMI from read 1 and adds them to header of read 2 (a unique output fastq is created).
+  
+* **je retag**
+  
+    extracts barcode(s) and UMI sequence(s) embedded in read names of a BAM file and migrate them to proper BAM tags.
 
 * **je clip**
 
 	to remove UMIs contained in reads of fastq files that do not need sample demultiplexing
 
+* **je markdupes**
+
+ 	filters BAM files for read duplicates taking UMIs into account.
+
 * **je demultiplex**
 
-	to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not)
+	to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not). Deprecated since version 2.0 (use *je debarcode* instead).
 
 * **je demultiplex-illu**
 
  	to demultiplex fastq files according to associated index files (contain the sample encoding barcodes).
- 	Reads can additionally contain UMIs (inline)
+    Reads can additionally contain UMIs (inline). Deprecated since version 2.0 (use *je debarcode* instead).
 
-* **je markdupes**
 
- 	to filter BAM files for read duplicates taking UMIs into account
 
 
 ### Distributions
@@ -45,7 +61,7 @@ Je currently offers 4 tools:
 
 * ``src/shell/je``
 
-    is the wrapper script to call ``java -jar je_1.0_bundle.jar``
+    is the wrapper script to call ``java -jar je_*_bundle.jar``
 
 * ``src/galaxy/``
 

dist/README.md

+1. Create a dir with :
+  * the je wrapper
+  * the log4j.xml
+  * the Je bundle jar
+  
+2. Make sure the je wrapper calls the correct jar 
+3. tar czf <tarname>.tar.gz <dirname>/* 
+  e.g. 
+  `tar czf je_2.0.RC.tar.gz je_2.0.RC/*`
\ No newline at end of file

dist/je

 #!/bin/sh
-# Wrapper around je_1.1_bundle.jar
+# Wrapper around je_*_bundle.jar
 
 # where are we stored ?
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 # echo $DIR
 # path to jar file to execute, this jar is supposed to be in the same dir as this script
-JAR_FILE=$DIR"/je_1.0_bundle.jar"
+JAR_FILE=$DIR"/je_2.0.RC_bundle.jar"
+
 
 # set default _JAVA_OPTIONS
 _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx4G -Xms256m'}

dist/je_2.0.RC/je

+#!/bin/sh
+# Wrapper around je_*_bundle.jar
+
+# where are we stored ?
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+# echo $DIR
+# path to jar file to execute, this jar is supposed to be in the same dir as this script
+JAR_FILE=$DIR"/je_2.0.RC_bundle.jar"
+
+# set default _JAVA_OPTIONS
+_JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx4G -Xms256m'}
+export _JAVA_OPTIONS
+
+# uncomment to change logging level using your own log4j.xml found in $DIR file
+# OPTS="-Dlog4j.configuration=file:$DIR/log4j.xml"
+
+java $OPTS -jar $JAR_FILE "$@"
+exit $?

dist/je_2.0.RC/log4j.xml

+<?xml version="1.0" encoding="UTF-8" ?>
+<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+
+<log4j:configuration xmlns:log4j="http://jakarta.apache.org/log4j/">
+
+	<appender name="CONSOLE" class="org.apache.log4j.ConsoleAppender">
+		<layout class="org.apache.log4j.PatternLayout">
+			<param name="ConversionPattern" value="%d{dd-MM-yy HH:mm:ss} %-5p [%t] %c{1}.%M(%L) | %m%n" />
+		</layout>
+	</appender>
+
+	
+	
+	<root>
+		<level value="INFO" /> 
+		<appender-ref ref="CONSOLE" />
+	</root>
+
+</log4j:configuration>

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>1.2</version>
+	<version>2.0.RC</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.regex.Pattern;
+
+import org.apache.commons.lang3.StringUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import htsjdk.samtools.fastq.FastqRecord;
+import htsjdk.samtools.util.FastqQualityFormat;
+
+/**
+ * 
+ * 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 in case of barcode, one might want to write the barcode or the read sequence corresponding to the looked up sample barcode.  
+ * 
+ * The possible keys are :<br/>
+ * <ul>
+ * <li>SAMPLEn  : refers to the SAMPLE slot with idx 'n' defined in the {@link ReadLayout} objects</li>
+ * <li>UMIn     : refers to the UMI slot with idx 'n' defined in the {@link ReadLayout} objects</li>
+ * <li>BARCODEn : refers to the sample barcode resolved from the read sequence found in the of the BARCODE slot with idx 'n' defined in the {@link ReadLayout} objects</li>
+ * <li>READBARn : refers to the read sequence found in the BARCODE slot with idx 'n' defined in the {@link ReadLayout} objects ; this is only valida in read name layout 
+ * i.e. read sequence always contain original sequence</li>
+ * </ul> 
+ * 
+ * Note that a short layout format can also be used like 'B1', 'U2', 'S1' or 'R1' instead of '<BARCODE1>' , '<UMI2>' , '<SAMPLE1>' and <READBAR>; 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);
+	
+	public static final String DEFAULT_READNAME_DELIMITOR = ":";
+	private static final String LONG_LAYOUT_REGEX = "^(<?(BARCODE|UMI|SAMPLE|READBAR)\\d+>?)+$";
+	private static final String SHORT_LAYOUT_REGEX = "^([BUSR]\\d+)+$";
+	
+	
+	
+	/**
+	 * char to use to delineate slots in read name ; if needed
+	 */
+	protected String readNameDelimitor = DEFAULT_READNAME_DELIMITOR;
+	
+	/**
+	 * Should the quality string be injected into read name together with READBAR and UMI slots ? 
+	 */
+	protected boolean withQualityInReadName = false;
+	
+
+	/**
+	 * 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;
+	
+	
+	/**
+	 * the {@link FastqQualityFormat} of the input fastq files
+	 */
+	protected FastqQualityFormat fastqQualityFormat = null;
+	
+
+	
+	
+	/**
+	 * @param readSequenceLayout the string representation of the output layout to use for the read sequence e.g. "S1"
+	 * @param readNameLayout the string representation of the output layout to use for the read name e.g. "B1U1S1" 
+	 * @param readLayouts the ordered {@link ReadLayout} objects defining how input fastq files are formatted
+	 * @param withQualityInReadName indicates if the Barcode/UMI quality should be injected in the read name together with their sequence
+	 * @param readNameDelimitor the character to use to split up the read name (':' is the default)
+	 * @param convertBarcodeToReadbar  if true all BARCODE slots are converted to READBAR in the readNameLayout (BARCODE == READBAR in readSequenceLayout)
+	 * @param fastqQualityFormat the {@link FastqQualityFormat} of the input fastq files
+	 */
+	public FastqWriterLayout(
+			final String readSequenceLayout, 
+			final String readNameLayout, 
+			final ReadLayout [] readLayouts, 
+			final boolean withQualityInReadName, 
+			final String readNameDelimitor, 
+			final boolean convertBarcodeToReadbar, 
+			final FastqQualityFormat fastqQualityFormat) {
+		
+		this.readNameLayout = (StringUtils.isBlank(readNameLayout) ? null : convertToShortLayout(readNameLayout));
+		this.readSequenceLayout = convertToShortLayout(readSequenceLayout);
+		this.readLayouts = readLayouts;
+		this.withQualityInReadName = withQualityInReadName;
+		this.readNameDelimitor = readNameDelimitor;
+		if(convertBarcodeToReadbar && readNameLayout!=null) {
+			this.readNameLayout = this.readNameLayout.replaceAll("B", "R");
+		}
+		this.fastqQualityFormat = fastqQualityFormat;
+		init(); //build all maps for easy lookup
+	}
+	
+
+	/**
+	 * @param readSequenceLayout the string representation of the output layout to use for the read sequence e.g. "S1"
+	 * @param readNameLayout the string representation of the output layout to use for the read name e.g. "B1U1S1" 
+	 * @param readLayouts the ordered {@link ReadLayout} objects defining how input fastq files are formatted
+	 * @param withQualityInReadName indicates if the Barcode/UMI quality should be injected in the read name together with their sequence
+	 * @param readNameDelimitor the character to use to split up the read name (':' is the default)
+	 * @param fastqQualityFormat the {@link FastqQualityFormat} of the input fastq files
+	 */
+	public FastqWriterLayout(final String readSequenceLayout, final String readNameLayout, final ReadLayout [] readLayouts, final boolean withQualityInReadName, final String readNameDelimitor, final FastqQualityFormat fastqQualityFormat) {
+		this(readSequenceLayout, readNameLayout, readLayouts, withQualityInReadName, readNameDelimitor, false, fastqQualityFormat);
+	}
+	
+	
+	/**
+	 * @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", "");
+			shortLayout = shortLayout.replaceAll("EADBAR", "");
+		}
+		log.debug("short layout : "+shortLayout);
+		return shortLayout;
+		
+	}
+
+	
+	/**
+	 * Assemble the {@link FastqRecord} that should be written in the output file according to the layout(s) ; this method should be used when a barcode has been matched
+	 * 
+	 * @param reads the {@link FastqRecord} from the input fastq files in the order matching the {@link ReadLayout} given at construction
+	 * @param sampleMatch a {@link SampleMatch} holding all the barcode matches
+	 * @return
+	 */
+	public FastqRecord assembleRecord( FastqRecord[] reads, SampleMatch sampleMatch ){
+		
+		FastqRecord rec = sequenceConsumer.assembleNewRead(reads);
+		String name = rec.getReadName(); 
+		if(readNameConsumer != null) 
+			name = readNameConsumer.assembleNewReadName(reads, sampleMatch);
+		
+		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 m a {@link SampleMatch} holding all the barcode matches  
+	 * @return
+	 */
+	public FastqRecord assembleRecord( FastqRecord read, SampleMatch m ){
+		return assembleRecord(new FastqRecord[]{read}, m);
+	}
+	
+	
+	
+	/**
+	 * 
+	 */