* 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
*
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@@ -62,8 +72,8 @@ public class FastqWriterLayout {
"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 "+
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@@ -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"