#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:
thrownewLayoutMalformedException("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","");
}
log.debug("short layout : "+shortLayout);
returnshortLayout;
}
/**
* 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 useReadSequenceForBarcodes dictates what to write in the read header layouts of the {@link FastqWriterLayout} for each BARCODE.
* When false, the matched barcode is used. When true, the exact read sequence extracted from the barcode slot is written
* @param m a {@link SampleMatch} holding all the barcode matches
thrownewLayoutMalformedException("FASTQ Output Layout for read sequence does not match expected short format (regex is :"+SHORT_LAYOUT_REGEX+")",this.readSequenceLayout);
thrownewLayoutMalformedException("FASTQ Output Layout for read name does not match expected short format (regex is :"+SHORT_LAYOUT_REGEX+")",this.readNameLayout);
"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 "+
"FATAL : We just reached a supposedly unreachable part of the code. Please report this bug to Je developpers indicating the options you used i.e. : \n "+
StringUtil.mergeArray(args," ")
);
System.exit(1);//error
}
}catch(Exceptione){
log.error(ExceptionUtil.getStackTrace(e));
System.exit(1);//error
}
}
protectedstaticStringgetUsage(){
return"Usage: je <command> [options] \n\n"+
"with command in : \n"
+"\t "+COMMAND_CLIP+" \t\t clips molecular barcodes from fastq sequence and places them in read name headers for further use in 'dupes' module\n"
+"\t "+COMMAND_MULTIPLEX+" \t\t demultiplex fastq file(s), with optional handling of molecular barcodes for further use in 'dupes' module\n"
+"\t "+COMMAND_MULTIPLEX_ILLUMINA+" \t demultiplex fastq file(s) using Illumina Index files, with optional handling of molecular barcodes for further use in 'dupes' module\n"
+"\t "+COMMAND_DEMULTIPLEX+" \t\t demultiplexes fastq file(s), with optional handling of molecular barcodes for further use in 'dupes' module\n"
+"\t "+COMMAND_MULTIPLEX+" \t\t demultiplexes fastq file(s) with Je 1.x implementation, with optional handling of molecular barcodes for further use in 'dupes' module\n"
+"\t "+COMMAND_MULTIPLEX_ILLUMINA+" \t demultiplexes fastq file(s) using Illumina Index files with Je 1.x implementation, with optional handling of molecular barcodes for further use in 'dupes' module\n"
+"\t "+COMMAND_DUPES+" \t\t removes read duplicates based on molecular barcodes found in read name headers (as produced by clip or plex)\n"
+"\t "+COMMAND_DROPSEQ+" \t\t clips cell barcode and UMI from read 1 and adds them to header of read 2. This command is for processing drop-seq results.\n"