2.0 RC version. je markdupes does not deal with UMI from BAM TAG (still

expected in read names)

.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

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_1.1_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>

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>Je</groupId>
 	<artifactId>Je</artifactId>
-	<version>2.0.beta</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>
 

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

@@ -34,6 +34,7 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import htsjdk.samtools.fastq.FastqRecord;
+import htsjdk.samtools.util.FastqQualityFormat;
 
 /**
  * 
@@ -112,24 +113,32 @@ public class FastqWriterLayout {
 	 */
 	protected ReadLayout [] readLayouts;
 	
+	
 	/**
-	 * @param readSequenceLayout
-	 * @param readNameLayout can be null when the read name should be reused unmodified
-	 * @param readLayouts
+	 * 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) {
-		this(readSequenceLayout, readNameLayout, readLayouts, withQualityInReadName, readNameDelimitor, false);
-	}
+	protected FastqQualityFormat fastqQualityFormat = null;
+	
+
+	
 	
 	/**
-	 * @param readSequenceLayout
-	 * @param readNameLayout
-	 * @param readLayouts
-	 * @param withQualityInReadName
-	 * @param readNameDelimitor
+	 * @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) {
+	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);
@@ -139,24 +148,23 @@ public class FastqWriterLayout {
 		if(convertBarcodeToReadbar && readNameLayout!=null) {
 			this.readNameLayout = this.readNameLayout.replaceAll("B", "R");
 		}
+		this.fastqQualityFormat = fastqQualityFormat;
 		init(); //build all maps for easy lookup
 	}
 	
 
-	
 	/**
-	 * @param readSequenceLayout
-	 * @param readNameLayout can be null when the read name should be reused unmodified
-	 * @param readLayout
+	 * @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 readLayout, final boolean withQualityInReadName, final String readNameDelimitor) {
-		this(readSequenceLayout, readNameLayout, new ReadLayout[]{ readLayout }, withQualityInReadName, readNameDelimitor, false);
+	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);
 	}
 	
-	public FastqWriterLayout(final String readSequenceLayout, final String readNameLayout, final ReadLayout readLayout, final boolean withQualityInReadName, final String readNameDelimitor, final boolean convertBarcodeToReadbar) {
-		this(readSequenceLayout, readNameLayout, new ReadLayout[]{ readLayout }, withQualityInReadName, readNameDelimitor, convertBarcodeToReadbar);
-	}
-
 	
 	/**
 	 * @param layout
@@ -186,36 +194,18 @@ public class FastqWriterLayout {
 
 	
 	/**
-	 * Assemble the {@link FastqRecord} that should be written in the output file according to the layout(s).
-	 * This method also use the read sequence to write BARCODE in read name
-	 * @param reads the {@link FastqRecord} from the input fastq files in the order matching the {@link ReadLayout} given at construction 
+	 * 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 ){
-		
-		FastqRecord rec = sequenceConsumer.assembleNewRead(reads);
-		String name = rec.getReadName(); 
-		if(readNameConsumer != null) 
-			name = readNameConsumer.assembleNewReadName(reads);
-		
-		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;
-	}
-
-	/**
-	 * 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 m a {@link SampleMatch} holding all the barcode matches
-	 * @return
-	 */
-	public FastqRecord assembleRecord( FastqRecord[] reads, SampleMatch m ){
+	public FastqRecord assembleRecord( FastqRecord[] reads, SampleMatch sampleMatch ){
 		
 		FastqRecord rec = sequenceConsumer.assembleNewRead(reads);
 		String name = rec.getReadName(); 
 		if(readNameConsumer != null) 
-			name = readNameConsumer.assembleNewReadName(reads, m);
+			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());
@@ -224,7 +214,7 @@ public class FastqWriterLayout {
 	
 	/**
 	 * Convenient wrapper for single end configuration
-	 * @param read the {@link FastqRecord} from the input fastq file
+	 * @param read the {@link FastqRecord} from the input fastq file 
 	 * @param m a {@link SampleMatch} holding all the barcode matches  
 	 * @return
 	 */
@@ -255,7 +245,7 @@ public class FastqWriterLayout {
 			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, this.withQualityInReadName, this.readNameDelimitor);
+			readNameConsumer = new ReadLayoutConsumer(this.readNameLayout, this.readLayouts, this.withQualityInReadName , this.readNameDelimitor, this.fastqQualityFormat);
 		}
 	}
 	

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

@@ -28,6 +28,8 @@ import java.util.Arrays;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import htsjdk.samtools.SAMUtils;
+
 public class JeTry {
 	private static Logger log = LoggerFactory.getLogger(JeTry.class);
 
@@ -36,9 +38,7 @@ public class JeTry {
 	}
 
 	public static void main(String[] args) {
-		System.out.println(JeUtils.toBytesThenPhred(
-				"26242516303031"
-				));
+		
 		
 	}
 

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

@@ -26,12 +26,23 @@ package org.embl.gbcs.je;
 import java.util.Set;
 import java.util.TreeSet;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import com.developpez.adiguba.shell.ProcessConsumer;
 
 import htsjdk.samtools.SAMUtils;
+import htsjdk.samtools.fastq.FastqReader;
+import htsjdk.samtools.util.FastqQualityFormat;
+import htsjdk.samtools.util.QualityEncodingDetector;
+import htsjdk.samtools.util.SolexaQualityConverter;
 
 public class JeUtils {
 
+	
+	private static Logger log = LoggerFactory.getLogger(JeUtils.class);
+
+	
 	/*
 	 * BC : for sample barcode, raw or corrected, with QT to store its quality string
 	 */
@@ -69,7 +80,7 @@ public class JeUtils {
 	public static final String SAMTAG_MI = "MI"; 
 	
 	
-	/**convert a string of quality numbers (each quality has 2 char) to the Phred String
+	/**convert a string of quality numbers in Phred Scale (each quality has 2 char) to the Standard Phred + 33 encoding
 	 * ie 
 	 * @param s
 	 * @return
@@ -85,6 +96,54 @@ public class JeUtils {
 	}
 	
 	
+	/** 
+	 * Based on the type of quality scores coming in, converts them to a numeric byte[] in phred scale. 
+	 */
+	public static void convertQualityToPhred(byte[] quals, final FastqQualityFormat version) {
+		switch (version)  {
+		case Standard:
+			SAMUtils.fastqToPhred(quals);
+			break ;
+		case Solexa:
+			SolexaQualityConverter.getSingleton().convertSolexaQualityCharsToPhredBinary(quals);
+			break ;
+		case Illumina:
+			SolexaQualityConverter.getSingleton().convertSolexa_1_3_QualityCharsToPhredBinary(quals);
+			break ;
+		}
+	}
+	
+	
+	 /**
+     * Looks at fastq input(s) and attempts to determine the proper quality format
+     *
+     * Closes the reader(s) by side effect
+     *
+     * @param readers readers on the input fastq files
+     * @param expectedQuality If provided, will be used for sanity checking. If left null, autodetection will occur
+     */
+    public static FastqQualityFormat determineQualityFormat(final FastqReader [] readers, final FastqQualityFormat expectedQuality) {
+        final QualityEncodingDetector detector = new QualityEncodingDetector();
+
+        //add all fastq readers
+        detector.add(QualityEncodingDetector.DEFAULT_MAX_RECORDS_TO_ITERATE, readers);
+        //close all readers
+        for (FastqReader reader : readers) {
+        		reader.close();
+		}
+        //
+        final FastqQualityFormat qualityFormat =  detector.generateBestGuess(QualityEncodingDetector.FileContext.FASTQ, expectedQuality);
+        //in case there is no expected quality and different options were possible, warn user
+        if (detector.isDeterminationAmbiguous()) {
+            log.warn("Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.");
+        }
+        
+        	log.info(String.format("Auto-detected quality format as: %s.", qualityFormat));
+
+        return qualityFormat;
+    }
+	
+	
 	/**
 	 * @return the result of executing whoami on the underlying OS 
 	 */

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

@@ -30,11 +30,13 @@ import java.util.TreeSet;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import org.embl.gbcs.je.demultiplexer.Demultiplexer;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import htsjdk.samtools.SAMUtils;
 import htsjdk.samtools.fastq.FastqRecord;
+import htsjdk.samtools.util.FastqQualityFormat;
 
 public class ReadLayoutConsumer {
 	private static Logger log = LoggerFactory.getLogger(ReadLayoutConsumer.class);
@@ -53,26 +55,36 @@ public class ReadLayoutConsumer {
 	String outPutLayout;
 	boolean withQualityInReadName;
 	String readNameDelimitor = ":";
-		 
+	FastqQualityFormat fastqQualityFormat = null;
 	
 	/**
-	 * @param outPutLayout in short format
-	 * @param readLayouts all ordered layout (order is as the reads are read from files)
+	 * Creates a simple ReadLayoutConsumer with default read name delimitor (':') and standard 
+	 * fastq quality format {@link FastqQualityFormat#Standard}. 
+	 * 
+	 * @param outPutLayout the string representation of the output layout e.g. "B1U1S1" 
+	 * @param readLayouts the ordered {@link ReadLayout} objects defining how input fastq files are formatted
+	 * 
 	 */
 	public ReadLayoutConsumer(String outPutLayout, ReadLayout [] readLayouts){
-		this(outPutLayout, readLayouts, false, ":");
+		this(outPutLayout, readLayouts, false, ":", FastqQualityFormat.Standard);
 	}
 	
+	
 	/**
-	 * @param outPutLayout in short format
-	 * @param readLayouts all ordered layout (order is as the reads are read from files)
+	 * Creates a ReadLayoutConsumer
+	 *  
+	 * @param outPutLayout the string representation of the output layout 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 ReadLayoutConsumer(String outPutLayout, ReadLayout [] readLayouts, boolean withQualityInReadName, String readNameDelimitor){
+	public ReadLayoutConsumer(String outPutLayout, ReadLayout [] readLayouts, boolean withQualityInReadName, String readNameDelimitor, final FastqQualityFormat fastqQualityFormat){
 		this.outPutLayout = outPutLayout;
 		this.readLayouts = readLayouts;
 		this.withQualityInReadName = withQualityInReadName;
 		this.readNameDelimitor = readNameDelimitor;
-		
+		this.fastqQualityFormat = fastqQualityFormat;
 		
 		Pattern sub = Pattern.compile("([BUSR])(\\d+)");
 		Matcher subMatcher = sub.matcher("");
@@ -142,19 +154,6 @@ public class ReadLayoutConsumer {
 
 
 	
-	/**
-	 * 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 
-	 * In this method, the read sequence is always used in BARCODE slots
-	 * 
-	 * @param reads the reads in order matching that of the {@link ReadLayout} array used at construction
-	 * 
-	 * @return
-	 */
-	public String assembleNewReadName(FastqRecord [] reads){
-		return assembleNewReadName(reads, null);
-	}
-	
 	
 	/**
 	 * Assemble a read name by concatenating the output layout to the original read name.  
@@ -183,54 +182,61 @@ public class ReadLayoutConsumer {
 			String subseq = null;
 			byte[] qualB = null;
 			int bestQual = 0;
-			if(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_READBAR:
-						_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;
-					}
-					byte[] _qualB = SAMUtils.fastqToPhred(_subqual);
-					int _qualsum = overallQuality( _qualB );
-					if(subseq == null || _qualsum > bestQual){
-						subseq = _subseq;
-						qualB = _qualB;
-						bestQual = _qualsum;
-					}
+
+			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:
+					// we init the subseq with the matched barcode directly
+					_subseq = m.getBarcodeMatches().get(slotIdx).barcode;
+					_subqual = rl.extractBarcode(readForLayout.getBaseQualityString(), slotIdx);
+					break;
+				case BYTECODE_READBAR:
+					_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;
+				}
+				byte[] _qualB = _subqual.getBytes();
+				int _qualsum = overallQuality( _qualB );
+				if(subseq == null || _qualsum > bestQual){
+					subseq = _subseq;
+					qualB = _qualB;
+					bestQual = _qualsum;
 				}
 			}
+
 			//concatenate to the growing name
 			newname += this.readNameDelimitor + subseq;
-			if(withQualityInReadName)
-				newname += qualityToNumberString(qualB);
+			if(withQualityInReadName) {			
+				newname += qualityToNumberString(qualB, this.fastqQualityFormat);
+			}
 			log.debug("header is now : "+newname);
 		}
 
 		return newname;
 	}
 
-	/*
-	 * returns a string made of 2-digits quality scores for injection in the read name 
+
+	/**
+	 * @param qualbytes byte representation of initial quality string 
+	 * @param fastqQualityFormat the encoding of these bytes
+	 * @return
 	 */
-	public synchronized static String qualityToNumberString(byte[] qualbytes) {
+	public synchronized static String qualityToNumberString(byte[] qualbytes, FastqQualityFormat fastqQualityFormat) {
+		JeUtils.convertQualityToPhred(qualbytes, fastqQualityFormat);
 		NumberFormat nf = NumberFormat.getIntegerInstance();
 		nf.setMinimumIntegerDigits(2);
 		StringBuffer sb = new StringBuffer(qualbytes.length*2);

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

@@ -41,6 +41,9 @@ public class SampleMatch {
 		 */
 		protected Map<Integer, BarcodeMatch> barcodeMatches;
 		
+		/**
+		 * A note to propagate for diagnostic file
+		 */
 		protected String diagnosticNote = "";
 		
 		public SampleMatch(String sample, Map<Integer, BarcodeMatch> barcodeMatches){

src/main/java/org/embl/gbcs/je/demultiplexer/Demultiplexer.java

@@ -836,7 +836,7 @@ public class Demultiplexer {
 		byte [] subseqBytes = readSlot.getReadBases();
 		byte [] qualBytes = readSlot.getBaseQualityString().getBytes();
 		log.debug("   Q bytes => "+Arrays.toString(qualBytes));
-		convertQuality(qualBytes, this.fastqQualityFormat);
+		JeUtils.convertQualityToPhred(qualBytes, this.fastqQualityFormat);
 		log.debug("   converted Q bytes => "+Arrays.toString(qualBytes));
 		
 		int numMismatchesInBestBarcode = readSlot.getReadLength() + 1; //init with max mismatch num + 1
@@ -920,22 +920,6 @@ public class Demultiplexer {
 	}
 
 	
-	/** 
-	 * Based on the type of quality scores coming in, converts them to a numeric byte[] in phred scale. 
-	 */
-	protected void convertQuality(byte[] quals, final FastqQualityFormat version) {
-		switch (version)  {
-		case Standard:
-			SAMUtils.fastqToPhred(quals);
-			break ;
-		case Solexa:
-			SolexaQualityConverter.getSingleton().convertSolexaQualityCharsToPhredBinary(quals);
-			break ;
-		case Illumina:
-			SolexaQualityConverter.getSingleton().convertSolexa_1_3_QualityCharsToPhredBinary(quals);
-			break ;
-		}
-	}
 	
 	
 	private FastqRecord[] nextReads(

src/main/java/org/embl/gbcs/je/jeclipper/Jeclipper.java

@@ -35,6 +35,7 @@ import org.embl.cg.utilitytools.utils.ExceptionUtil;
 import org.embl.cg.utilitytools.utils.FileUtil;
 import org.embl.cg.utilitytools.utils.StringUtil;
 import org.embl.gbcs.je.FastqWriterLayout;
+import org.embl.gbcs.je.JeUtils;
 import org.embl.gbcs.je.JemultiplexerFastqWriterFactory;
 import org.embl.gbcs.je.Jexception;
 import org.embl.gbcs.je.ReadLayout;
@@ -44,6 +45,7 @@ import org.slf4j.LoggerFactory;
 import htsjdk.samtools.fastq.FastqReader;
 import htsjdk.samtools.fastq.FastqRecord;
 import htsjdk.samtools.fastq.FastqWriter;
+import htsjdk.samtools.util.FastqQualityFormat;
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.CommandLineProgramProperties;
 import picard.cmdline.Option;
@@ -187,6 +189,14 @@ public class Jeclipper extends CommandLineProgram {
 			)
 	public String READ_NAME_SEPARATOR_CHAR = DEFAULT_READ_NAME_SEPARATOR_CHAR;
 	
+	@Option(shortName="V", optional = true,
+			printOrder=190,
+			doc="A value describing how the quality values are encoded in the fastq files.  Either 'Solexa' for pre-pipeline 1.3 " +
+					"style scores (solexa scaling + 66), 'Illumina' for pipeline 1.3 and above (phred scaling + 64) or 'Standard' for phred scaled " +
+					"scores with a character shift of 33.  If this value is not specified (or 'null' is given), the quality format is assumed to be will the 'Standard' for phred scale.\n"
+			)
+	public FastqQualityFormat QUALITY_FORMAT = null;
+
 	
 	@Option(shortName="TEST", optional = true,
 			printOrder=210,
@@ -237,6 +247,7 @@ public class Jeclipper extends CommandLineProgram {
 			_names.add(f.getAbsolutePath());
 		}
 			
+		
 		/*
 		 * Validate O
 		 * if not given, init to current dir else ensure the dir exists
@@ -256,6 +267,22 @@ public class Jeclipper extends CommandLineProgram {
 		}
 		
 		
+		/*
+		 * Check quality format
+		 */
+		if (QUALITY_FORMAT == null) { // we assume it s Standard
+			FastqReader [] readers = new FastqReader[FASTQ.size()];
+			int i = 0;
+			for(File f : FASTQ){
+				readers[i++] = new FastqReader(f);
+			}
+			QUALITY_FORMAT = JeUtils.determineQualityFormat(readers, FastqQualityFormat.Standard);
+			log.info( String.format("Auto-detected quality encoding format as '%s'. Please set V option explicitely if not correct.", QUALITY_FORMAT) );
+		} else {
+			log.info(String.format("Quality encoding format set to %s by user.", QUALITY_FORMAT));
+		}
+		
+		
 		/*
 		 * parse read layout, we must have one per input FASTQ
 		 * 
@@ -320,7 +347,7 @@ public class Jeclipper extends CommandLineProgram {
 				 * here BARCODE (or B) always mean READBAR (or R). We need to convert BARCODE to READBAR to
 				 *  make sure the FastqWriterLayout bahaves properly
 				 */
-				outLayouts[j] = new FastqWriterLayout(seqLayout, headerLayout, readLayouts, WITH_QUALITY_IN_READNAME, READ_NAME_SEPARATOR_CHAR, true);
+				outLayouts[j] = new FastqWriterLayout(seqLayout, headerLayout, readLayouts, WITH_QUALITY_IN_READNAME, READ_NAME_SEPARATOR_CHAR, true, this.QUALITY_FORMAT);
 			}catch(Exception e){
 				log.error(ExceptionUtil.getStackTrace(e));
 				return new String[]{e.getMessage()};
@@ -480,7 +507,7 @@ public class Jeclipper extends CommandLineProgram {
 				for (int i = 0; i < fastqWriters.size(); i++) {
 					//prepare the output according to output layout
 					log.debug("Writing in output idx "+(i+1));
-					FastqRecord rec = outLayouts[i].assembleRecord( reads );
+					FastqRecord rec = outLayouts[i].assembleRecord( reads , null);
 					fastqWriters.get(i).write(rec);
 				}
 			}

src/main/java/org/embl/gbcs/je/jedropseq/Jedropseq.java

@@ -38,6 +38,7 @@ import htsjdk.samtools.SAMUtils;
 import htsjdk.samtools.fastq.FastqReader;
 import htsjdk.samtools.fastq.FastqRecord;
 import htsjdk.samtools.fastq.FastqWriter;
+import htsjdk.samtools.util.FastqQualityFormat;
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.CommandLineProgramProperties;
 import picard.cmdline.Option;
@@ -90,13 +91,13 @@ public class Jedropseq extends CommandLineProgram {
 
 	@Option(shortName="F1", optional = false, 
 			printOrder=10, 
-			doc="Input fastq file (optionally gzipped) for first read. This read contains the cell barcode followed by the UMI"
+			doc="Input fastq file (optionally gzipped) for first read. This read contains the cell barcode followed by the UMI. Quality encoding must be Phred+33 (Standard)."