commit before refactoring to introduce the READBAR concept

.gitignore

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

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

@@ -49,11 +49,21 @@ import htsjdk.samtools.fastq.FastqRecord;
  *   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.  
  * 
- * Note that a short layout format can also be used like 'B1', 'U2', 'S1'' instead of '<BARCODE1>' , '<UMI2>' and '<SAMPLE1>' ; respectively. 
+ * 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</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.  
+ * Technically speaking, the short layout format is the only one used.  
  * 
  * @author girardot
  *
@@ -62,8 +72,8 @@ public class FastqWriterLayout {
 
 	private static Logger log = LoggerFactory.getLogger(FastqWriterLayout.class);
 	
-	private static final String LONG_LAYOUT_REGEX = "^(<?(BARCODE|UMI|SAMPLE)\\d+>?)+$";
-	private static final String SHORT_LAYOUT_REGEX = "^([BUS]\\d+)+$";
+	private static final String LONG_LAYOUT_REGEX = "^(<?(BARCODE|UMI|SAMPLE|READBAR)\\d+>?)+$";
+	private static final String SHORT_LAYOUT_REGEX = "^([BUSR]\\d+)+$";
 	
 	
 	
@@ -143,12 +153,32 @@ public class FastqWriterLayout {
 			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 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 
+	 * 
+	 * @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)

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

@@ -34,6 +34,7 @@ import org.embl.gbcs.je.jedropseq.Jedropseq;
 import org.embl.gbcs.je.jeduplicates.MarkDuplicatesWithMolecularCode;
 import org.embl.gbcs.je.jemultiplexer.Jemultiplexer;
 import org.embl.gbcs.je.jemultiplexer.JemultiplexerIllumina;
+import org.embl.gbcs.je.retag.TagFromReadName;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -50,6 +51,7 @@ public class Je  {
 	private static Logger log = LoggerFactory.getLogger(Je.class);
 
 	
+	public static final String COMMAND_RETAG = "retag"; 
 	public static final String COMMAND_DEMULTIPLEX = "debarcode"; 
 	public static final String COMMAND_DROPSEQ = "dropseq"; 
 	public static final String COMMAND_CLIP = "clip"; 
@@ -64,8 +66,9 @@ public class Je  {
 		ALLOWED_COMMANDS.add(COMMAND_DUPES);
 		ALLOWED_COMMANDS.add(COMMAND_MULTIPLEX);
 		ALLOWED_COMMANDS.add(COMMAND_MULTIPLEX_ILLUMINA);
-		ALLOWED_COMMANDS.add(COMMAND_DROPSEQ);
+		//ALLOWED_COMMANDS.add(COMMAND_DROPSEQ);
 		ALLOWED_COMMANDS.add(COMMAND_DEMULTIPLEX);
+		ALLOWED_COMMANDS.add(COMMAND_RETAG);
 		
 	}
 	
@@ -125,6 +128,9 @@ public class Je  {
 			else if(option.equalsIgnoreCase(COMMAND_DROPSEQ)){
 				new Jedropseq().instanceMainWithExit(argv);
 			}
+			else if(option.equalsIgnoreCase(COMMAND_RETAG)){
+				new TagFromReadName().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 "+
@@ -146,7 +152,8 @@ public class Je  {
 				+"\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"
+				//+"\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"
+				+"\t "+COMMAND_RETAG+"    \t\t extracts barcode and UMI sequence(s) embedded in read names and tag reads with proper BAM tag.\n"
 				+"\n"
 				+"Version : "+getVersion()
 				;

src/main/java/org/embl/gbcs/je/JeTry.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.FastqReader;
+import htsjdk.samtools.fastq.FastqRecord;
+import htsjdk.samtools.util.FastqQualityFormat;
+import htsjdk.samtools.util.QualityEncodingDetector;
+import htsjdk.samtools.util.SolexaQualityConverter;
+
+import java.io.File;
+import java.util.Arrays;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class JeTry {
+	private static Logger log = LoggerFactory.getLogger(JeTry.class);
+
+	public JeTry() {
+		// TODO Auto-generated constructor stub
+	}
+
+	public static void main(String[] args) {
+		String f = "/g/furlong/incoming/2017-06-28-000000000-B954B/000000000-B954B_precap_allpromV2_17s003049-1-1_Ghavi-helm_lane117s003049_1_sequence.txt.gz";
+		FastqReader reader = new FastqReader(new File(f));
+		FastqQualityFormat QUALITY_FORMAT = QualityEncodingDetector.detect(100000, reader);
+		log.info(String.format("Auto-detected quality encoding format as: %s.", QUALITY_FORMAT));
+		
+		FastqRecord r  =reader.iterator().next();
+		System.out.println(r.toFastQString());
+		System.out.println(r.getBaseQualityString());
+
+		byte [] bites = Arrays.copyOf( r.getBaseQualityString().getBytes() , r.getBaseQualityString().getBytes().length);
+		System.out.println(Arrays.toString( bites ));
+		SAMUtils.fastqToPhred(bites);
+		System.out.println(Arrays.toString( bites ));
+		
+		bites = Arrays.copyOf( r.getBaseQualityString().getBytes() , r.getBaseQualityString().getBytes().length);
+		System.out.println(Arrays.toString( bites ));
+		SolexaQualityConverter.getSingleton().convertSolexa_1_3_QualityCharsToPhredBinary(bites);
+		System.out.println(Arrays.toString( bites ));
+		
+		
+	}
+
+}

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

@@ -48,7 +48,7 @@ import org.slf4j.LoggerFactory;
  * <li> When no length ('x') is specified, all the sequence till the end is considered ; it only possible to use the 'x' 
  * shortcut in the last block of a layout</li>
  * <li> When a negative value is given in place of length (e.g. '<BLOCKCODEn:-2>'), all but the last x (2 in the 
- * '<BLOCKCODEn:-2>' example) bases ; a negative length value is only acceptedin the last block of a layout</li>
+ * '<BLOCKCODEn:-2>' example) bases ; a negative length value is only accepted in the last block of a layout</li>
  * </ul>
  * 
  * <br/>
@@ -152,6 +152,7 @@ public class ReadLayout {
 	}
 	
 	/**
+	 * change
 	 * Process the layout and initialize useful variables
 	 */
 	public void parseLayout(){

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

@@ -27,6 +27,7 @@ import htsjdk.samtools.SAMUtils;
 import htsjdk.samtools.fastq.FastqRecord;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Set;
 import java.util.TreeSet;
 import java.util.regex.Matcher;
@@ -122,6 +123,24 @@ 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){
+
+		boolean[] useReadSequenceForBarcodes = new boolean[reads.length];
+		Arrays.fill(useReadSequenceForBarcodes, true);
+		return assembleNewReadName(reads, useReadSequenceForBarcodes, null);
+	}
+	
+	
 	/**
 	 * 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 
@@ -150,7 +169,7 @@ public class ReadLayoutConsumer {
 			 */
 			String subseq = null;
 			int bestQual = 0;
-			if(!useReadSequenceForBarcodes[slotIdx-1] && slotTypeCode == BYTECODE_BARCODE){
+			if(slotTypeCode == BYTECODE_BARCODE && !useReadSequenceForBarcodes[slotIdx-1] ){
 				// we init the subseq with the matched barcode directly
 				subseq = m.getBarcodeMatches().get(slotIdx).barcode;
 			}else{
@@ -208,7 +227,7 @@ public class ReadLayoutConsumer {
 			byte slotTypeCode = slotCodes.get(i);
 			int slotIdx = this.slotIdx.get(i); 
 
-			log.debug("gettign info for slot code "+slotTypeCode+" with idx "+slotIdx);
+			log.debug("getting 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
 			 */

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

@@ -41,12 +41,19 @@ public class SampleMatch {
 		 */
 		protected Map<Integer, BarcodeMatch> barcodeMatches;
 		
+		protected String diagnosticNote = "";
 		
 		public SampleMatch(String sample, Map<Integer, BarcodeMatch> barcodeMatches){
 			this.sample= sample;
 			this.barcodeMatches = barcodeMatches;
 		}
 
+		public SampleMatch(String sample, Map<Integer, BarcodeMatch> barcodeMatches, String diagnosticNote){
+			this.sample= sample;
+			this.barcodeMatches = barcodeMatches;
+			this.diagnosticNote = diagnosticNote;
+		}
+
 
 		/**
 		 * @return the sample
@@ -64,6 +71,22 @@ public class SampleMatch {
 		}
 
 
+		/**
+		 * @return the diagnosticNote
+		 */
+		public String getDiagnosticNote() {
+			return diagnosticNote;
+		}
+
+
+		/**
+		 * @param diagnosticNote the diagnosticNote to set
+		 */
+		public void setDiagnosticNote(String diagnosticNote) {
+			this.diagnosticNote = diagnosticNote;
+		}
+
+
 		/**
 		 * @param sample the sample to set
 		 */

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

@@ -30,6 +30,7 @@ import htsjdk.samtools.util.QualityEncodingDetector;
 
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -87,7 +88,8 @@ public class Jedemultiplex extends CommandLineProgram {
 	protected static final String DEFAULT_METRICS_FILE_NAME = "jemultiplexer_out_stats.txt";
 	protected static final String DEFAULT_READ_NAME_SEPARATOR_CHAR = ":";
 	protected static final String DEFAULT_USE_ORIGINAL_BARCODE_SEQUENCE = "0";
-
+	protected static final boolean DEFAULT_STRICT = false;
+	
 	protected static final boolean DEFAULT_ADD_SEQUENCE_LAYOUT_IN_OUTPUT_FILENAME = false;
 
 	protected static final boolean DEFAULT_ADD_HEADER_LAYOUT_IN_OUTPUT_FILENAME = false;
@@ -304,6 +306,14 @@ public class Jedemultiplex extends CommandLineProgram {
 	// array  associated with MIN_BASE_QUALITY (after parsing) ; with a length that of the different barcode number found in the barcode file
 	int [] min_base_qualities;
 
+	@Option(shortName="S", optional = true,
+			printOrder=85,
+			doc="When reads have redundant BARCODE slots, this option tells how to handle situation when the read sequence do not resolve to the same sample.\n"
+					+" When true, the read pair is always 'unassigned'.\n"
+					+" When false, the read pair is assigned to the sample with the lowest overall mismatch sum\n"
+			)
+	public boolean STRICT = false;
+	
 	@Option(shortName = "O", optional = true,
 			printOrder=90,
 			doc="Output directory. By default, output files are written in running directory.\n")
@@ -951,8 +961,7 @@ public class Jedemultiplex extends CommandLineProgram {
 	private List<String> customEmbaseCommandLineValidation() {
 		//error messages to be accumulated
 		List<String> messages = new ArrayList<String>();
-		
-		
+			
 		OUTPUT_DIR = null;
 		GZIP_OUTPUTS=true;
 		CREATE_MD5_FILE = true;
@@ -964,12 +973,18 @@ public class Jedemultiplex extends CommandLineProgram {
 			String ufname= FileUtil.removeExtension( f.getName() ) + "_unassigned-reads"+".txt.gz" ;
 			unassignedFilePathes.add(ufname);
 		}
-		
-		
+				
 		/*
 		 * Get information from emBASE 
 		 */		
 		
+		//try load properties
+		try {
+			ApplicationConfiguration.init();
+		} catch (IOException e) {
+			log.error("Failed to read properties from property file.");
+			throw new RuntimeException(e);
+		}
 		//Determine the caller
 		String username = System.getProperty("user.name");
 		//check user is not trying to trick me with a -Duser.name=another user!
@@ -1099,7 +1114,7 @@ public class Jedemultiplex extends CommandLineProgram {
 							"Are you sure this lane has been successfully uploaded to emBASE ?\nIf so, please contact emBASE admins.";
 					log.debug(mess);
 					if(TEST_MODE_STOP_AFTER_PARSING){
-						log.debug("TEST MODE : Setting fake dir for "+lib.getName());
+						log.info("TEST MODE : Setting fake dir for "+lib.getName());
 						lib.setSampleDir ( EmBaseDatabaseFacade.getFakeSampleDir(lib.getName(), lib.getId()) );//does not exist, just fake for test
 					}
 					else{
@@ -1110,17 +1125,22 @@ public class Jedemultiplex extends CommandLineProgram {
 					//update lib.getSampleDir with fastq sub-dir
 					File fastqDir = new File(lib.getSampleDir(), "fastq");
 					if(!fastqDir.exists() || !fastqDir.canWrite()){
-						String mess = "The 'fastq' dir under the library dir  "+lib.getSampleDir().getAbsolutePath()
-								+" is either not existing OR not writable.\n";
-						if(!fastqDir.exists()){
-							mess+="The storage architecture is not ready. Are you sure this lane has been successfully uploaded to emBASE ?\nIf so, please contact emBASE admins.";
+						if(!TEST_MODE_STOP_AFTER_PARSING){
+							String mess = "The 'fastq' dir under the library dir  "+lib.getSampleDir().getAbsolutePath()
+									+" is either not existing OR not writable.\n";
+							if(!fastqDir.exists()){
+								mess+="The storage architecture is not ready. Are you sure this lane has been successfully uploaded to emBASE ?\nIf so, please contact emBASE admins.";
+							}
+							else{
+								mess+="The fastq storage file has been already locked to prevent further modifications.\n" +
+										"Please contact emBASE admins if you think this should not be the case.";
+							}
+							log.debug(mess);
+							messages.add(mess);
+						} else {
+							lib.setSampleDir( EmBaseDatabaseFacade.TMP_DIR );
+							log.info("TEST MODE : Setting fake sample dir to "+EmBaseDatabaseFacade.TMP_DIR);
 						}
-						else{
-							mess+="The fastq storage file has been already locked to prevent further modifications.\n" +
-									"Please contact emBASE admins if you think this should not be the case.";
-						}
-						log.debug(mess);
-						messages.add(mess);
 					}else{
 						lib.setSampleDir( fastqDir );
 					}
@@ -1142,7 +1162,11 @@ public class Jedemultiplex extends CommandLineProgram {
 		 */
 		PrintWriter pw = null;
 		try{
-			BARCODE_FILE = getBarcodeFileTmpLocation(FASTQ.get(0), username, runStatDir);
+			BARCODE_FILE = getBarcodeFileTmpLocation(
+					FASTQ.get(0), 
+					username, 
+					(TEST_MODE_STOP_AFTER_PARSING ? EmBaseDatabaseFacade.TMP_DIR : runStatDir)
+					);
 			if(BARCODE_FILE.exists()){
 				log.warn("The barcode file already exists and will be overwritten : "+BARCODE_FILE.getAbsolutePath());
 			}
@@ -1152,7 +1176,6 @@ public class Jedemultiplex extends CommandLineProgram {
 				File fastq1 = getDemultiplexedFile(lib, 1 , GZIP_OUTPUTS);
 				File fastq2 = getDemultiplexedFile(lib, 2 , GZIP_OUTPUTS);
 				
-				
 				/*
 				 * check if file already exists , the test on the length is meant to avoid considering a 'fake' file as a real file
 				 * we indeed create such files to prepare the architecture
@@ -1215,7 +1238,7 @@ public class Jedemultiplex extends CommandLineProgram {
 					outLayouts, 
 					this.unassignedFiles, 
 					this.metricsFile, 
-					this.QUALITY_FORMAT, 
+					this.QUALITY_FORMAT,
 					this.GZIP_OUTPUTS, 
 					this.CREATE_MD5_FILE);
 			
@@ -1226,6 +1249,7 @@ public class Jedemultiplex extends CommandLineProgram {
 					min_mismatch_deltas, 
 					min_base_qualities,
 					useOriginalSequenceForBarcode,
+					STRICT,
 					WRITER_FACTORY_USE_ASYNC_IO, 
 					bcDiagFile);
 			

src/main/java/org/embl/gbcs/je/jeduplicates/MarkDuplicatesWithMolecularCode.java

@@ -54,6 +54,7 @@ import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
 import java.util.TreeSet;
+import java.util.regex.Pattern;
 
 import org.apache.commons.lang3.StringUtils;
 import org.embl.cg.utilitytools.utils.FileUtil;
@@ -80,8 +81,8 @@ import picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap;
 				+ " account molecular barcodes (Unique Molecular Identifiers or UMIs) found in read header. " 
 				+ "All records are then either written to the output file with the duplicate records flagged or trashed.\n"
 				+"Example :\n"
-				+"\t je markdupes INPUT=file_with_dupes.bam OUPUT=result.bam MM=1", 
-		usageShort = "je markdupes INPUT=file_with_dupes.bam OUPUT=result.bam MM=1", 
+				+"\t je markdupes INPUT=file_with_dupes.bam OUTPUT=result.bam MM=1", 
+		usageShort = "je markdupes INPUT=file_with_dupes.bam OUTPUT=result.bam MM=1", 
 		programGroup = SamOrBam.class
 		)
 public class MarkDuplicatesWithMolecularCode extends AbstractMarkDuplicatesCommandLineProgram {
@@ -210,8 +211,6 @@ public class MarkDuplicatesWithMolecularCode extends AbstractMarkDuplicatesComma
 	private int numDuplicateIndices = 0;
 
 	private LibraryIdGenerator libraryIdGenerator = null; // this is initialized in buildSortedReadEndLists
-
-	
 	
 	public MarkDuplicatesWithMolecularCode() {
 		super();
@@ -223,6 +222,42 @@ public class MarkDuplicatesWithMolecularCode extends AbstractMarkDuplicatesComma
 		new MarkDuplicatesWithMolecularCode().instanceMainWithExit(args);
 	}
 
+	
+	
+	private void initReadNameRegexFromRead() {
+		
+		//teh base regex to which will had as many ":[ATGCUNatgcun]+" slots as needed
+		String baseRegex = "(?:.*:)?([0-9]+)[^:]*:([0-9]+)[^:]*:([0-9]+)[^:]*";
+		
+		final SamHeaderAndIterator headerAndIterator = openInputs();
+		final CloseableIterator<SAMRecord> iterator = headerAndIterator.iterator;
+		SAMRecord rec = null;
+		//peek a record
+		while (iterator.hasNext()) {
+			rec = iterator.next();
+			break;
+		}
+		iterator.close();
+		//get read name
+		String name = rec.getReadName();
+		String [] tokens = name.split(":");
+		//start from end : how many slots match a barcode ?
+		int n=0;
+		for(int p = tokens.length -1 ; p>0 ;p-- ){
+			if(Pattern.matches("[ATGCUNatgcun]+", tokens[p]))
+				n++;
+		}
+		
+		for(int i = 0 ; i< n; i++){
+			baseRegex += ":[ATGCUNatgcun]+";
+		}
+		
+		
+		log.debug("READ_NAME_REGEX initialized to "+baseRegex);
+		this.READ_NAME_REGEX = baseRegex;
+	}
+	
+	
 	/**
 	 * Main work method.  Reads the BAM file once and collects sorted information about
 	 * the 5' ends of both ends of each read (or just one end in the case of pairs).
@@ -234,6 +269,23 @@ public class MarkDuplicatesWithMolecularCode extends AbstractMarkDuplicatesComma
 		IOUtil.assertFileIsWritable(OUTPUT);
 		IOUtil.assertFileIsWritable(METRICS_FILE);
 
+		
+		/*
+		 * SET READ_NAME_REGEX to a proper value IF it was not given in the command line
+		 * => Reasoning on command line for READ_NAME_REGEX option
+		 */
+		if(!this.getCommandLine().contains("READ_NAME_REGEX")){
+			/*
+			 * we reset the default READ_NAME_REGEX to accommodate the additional barcode slots added to the read name
+			 * but only it the separator used was ':' and SLOTS or TSLOTS are not null
+			 */
+			if(this.SPLIT_CHAR.equals(':')){ 
+				initReadNameRegexFromRead();
+			}
+			//else the default regex should still work
+		}
+		
+		
 		/*
 		 * Molecular Barcode Support 
 		 * Initialize the MolecularBarcodeFinder
@@ -361,8 +413,7 @@ public class MarkDuplicatesWithMolecularCode extends AbstractMarkDuplicatesComma
 					++metrics.READ_PAIRS_EXAMINED; // will need to be divided by 2 at the end
 				}
 
-
-				if (recordInFileIndex == nextDuplicateIndex) {
+ 				if (recordInFileIndex == nextDuplicateIndex) {
 					rec.setDuplicateReadFlag(true);
 
 					// Update the duplication metrics
@@ -419,6 +470,7 @@ public class MarkDuplicatesWithMolecularCode extends AbstractMarkDuplicatesComma
 			} 
 			
 			
+
 			if (!this.REMOVE_DUPLICATES || !rec.getDuplicateReadFlag()) {
 				if (PROGRAM_RECORD_ID != null) {
 					rec.setAttribute(SAMTag.PG.name(), chainedPgIds.get(rec.getStringAttribute(SAMTag.PG.name())));
@@ -844,6 +896,7 @@ public class MarkDuplicatesWithMolecularCode extends AbstractMarkDuplicatesComma
 							best = end;
 						}
 					}
+
 				}
 				
 				//flag all reads duplicates but best

src/main/java/org/embl/gbcs/je/jeduplicates/ReadEndsForMarkDuplicatesWithMolecularCode2.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.jeduplicates;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.StringUtils;
+
+import htsjdk.samtools.util.StringUtil;
+import picard.sam.markduplicates.util.ReadEndsForMarkDuplicates;
+
+public class ReadEndsForMarkDuplicatesWithMolecularCode2 extends
+		ReadEndsForMarkDuplicates implements MolecularCodedReadEnds{
+
+	/*
+    What do we need to store you ask?  Well, we need to store:
+       - byte: orientation
+       - short: libraryId, readGroup, tile, x, y, score
+       - int: read1ReferenceIndex, read1Coordinate, read2ReferenceIndex, read2Coordinate, code length
+       - long: read1IndexInFile, read2IndexInFile
+       - byte array for code : fix it to 20, should be a max here
+     */
+	public static final int SIZE_OF = (1 * 1) + (5 * 2) + (4 * 5) + (8 * 2) + 1
+            + 8 + // last 8 == reference overhead
+            + 20 + //arbitrary byte array for code
+            13; // This is determined experimentally with JProfiler
+	
+	protected byte[] molecularCodeArr  = null;
+	
+	public void setMolecularCode(String code){
+		molecularCodeArr = StringUtil.stringToBytes(code.toUpperCase());
+	}
+	
+	/**
+	 * This is only meant to be used by the Codec. We don t want people to use this ie 
+	 * we want to make sure they use the string version so that we ensure codes are set upper case 
+	 * @param molecularCodeArr
+	 */
+	protected void setMolecularCode(byte[] molecularCodeArr){
+		this.molecularCodeArr = molecularCodeArr;
+	}
+
+	/**
+	 * @return the molecularCode
+	 */
+	public String getMolecularCode() {
+		return StringUtil.bytesToString(molecularCodeArr);
+	}
+	
+	/**
+	 * @param codelen length of an individual code. Each code is supposed to have the same length
+	 * @return the molecularCodes
+	 */
+	public List<String> getMolecularCodes(int codelen) {
+		int codenumber = molecularCodeArr.length / codelen;
+		List<String> codes = new ArrayList<String>(codenumber);
+		for(int i = 0 ; i < codenumber; i++){
+			codes.add(
+					StringUtil.bytesToString(molecularCodeArr, i*codelen, codelen)
+					);
+		}
+		return codes;
+	}
+	
+
+	/**
+	 * @return the molecularCodeArr
+	 */
+	public byte[] getMolecularCodeArr() {
+		return molecularCodeArr;
+	}
+
+	public String toString(){
+		String s = "RG="+readGroup+" ; "+tile+":"+x+":"+y+" ; orientation="+orientation+" ; paired="+(isPaired()?"1":"0")+" \n "
+				+"   R1-ref="+read1ReferenceIndex + ", R1-coor="+read1Coordinate +", idx="+read1IndexInFile+" \n "
+				+"   R2-ref="+read2ReferenceIndex + ", R2-coor="+read2Coordinate +", idx="+read2IndexInFile+" \n ";
+				
+		return s;
+	}
+	
+}

src/test/java/org/embl/gbcs/je/jeclipper/JeclipperTest.java

@@ -40,14 +40,14 @@ public class JeclipperTest {
 	private static Logger log = Logger.getLogger(JeclipperTest.class);
 
 
-	//@After
+	@After
 	public void cleanUpResultFiles(){
 		try {
 			File f1 = new File(JeclipperTest.class.getResource("file_1_sequence.txt").toURI());
 
 			File outdir = f1.getParentFile();
 			String [] fnames = new String []{
-					"file_1_sequence_out.txt", "file_2_sequence_out.txt"
+					"out_1.txt", "out_2.txt"
 			};
 
 			for (String fname : fnames) {
@@ -80,14 +80,12 @@ public class JeclipperTest {
 			File outdir = f1.getParentFile();
 
 			String[] argv = new String[] {
-					"F1="+f1.getAbsolutePath(), 
-					"F2="+f2.getAbsolutePath(),