97765dcefa668e25dbb48c96b7e99442db524038,rnaseq/src/run_SamToFastq.py,,,#,19

Before Change

    subprocess.check_call("gzip -"+args.gzip+" -c < read0_pipe > "+fastq0+" &", shell=True)

    // SamToFastq (write to pipes)
    subprocess.check_call("java -jar -Xmx"+args.memory+"g "+args.jar+" SamToFastq INPUT="+args.bam_file\
        +" INCLUDE_NON_PF_READS="+args.include_non_pf_reads\
        +" INCLUDE_NON_PRIMARY_ALIGNMENTS="+args.include_non_primary_alignments\
        +" VALIDATION_STRINGENCY=SILENT FASTQ=read1_pipe SECOND_END_FASTQ=read2_pipe UNPAIRED_FASTQ=read0_pipe", shell=True)

    // Delete named pipes
    subprocess.check_call("rm read1_pipe read2_pipe read0_pipe", shell=True)

After Change

        +" INCLUDE_NON_PRIMARY_ALIGNMENTS="+args.include_non_primary_alignments\
        +" VALIDATION_STRINGENCY=SILENT FASTQ=read1_pipe SECOND_END_FASTQ=read2_pipe UNPAIRED_FASTQ=read0_pipe"
    if args.reference_fasta is not None:
        cmd += " REFERENCE_SEQUENCE={}".format(args.reference_fasta)
    subprocess.check_call(cmd, shell=True)

    // Delete named pipes
    subprocess.check_call("rm read1_pipe read2_pipe read0_pipe", shell=True)

Instances