def picard_fastq_to_bam(picard, fastq_one, fastq_two, out_dir, names, order="queryname"):
    """Convert fastq file(s) to BAM, adding sample, run group and platform information.
    """
    out_bam = os.path.join(out_dir, "%s-fastq.bam" %
                           os.path.splitext(os.path.basename(fastq_one))[0])
    if not file_exists(out_bam):
        with tx_tmpdir(picard._config) as tmp_dir:
            with file_transaction(picard._config, out_bam) as tx_out_bam:
                opts = [("FASTQ", fastq_one),
                        ("READ_GROUP_NAME", names["rg"]),
                        ("SAMPLE_NAME", names["sample"]),
                        ("PLATFORM_UNIT", names["pu"]),
                        ("PLATFORM", names["pl"]),
                        ("TMP_DIR", tmp_dir),
                        ("OUTPUT", tx_out_bam),
                        ("SORT_ORDER", order)]
                if fastq_two:
                    opts.append(("FASTQ2", fastq_two))
                picard.run("FastqToSam", opts)
    return out_bam
def picard_fastq_to_bam ( picard , fastq_one , fastq_two , out_dir , names , order = "queryname" ) : out_bam = os . path . join ( out_dir , "%s-fastq.bam" % os . path . splitext ( os . path . basename ( fastq_one ) ) [ 0 ] ) if not file_exists ( out_bam ) : with tx_tmpdir ( picard . _config ) as tmp_dir : with file_transaction ( picard . _config , out_bam ) as tx_out_bam : opts = [ ( "FASTQ" , fastq_one ) , ( "READ_GROUP_NAME" , names [ "rg" ] ) , ( "SAMPLE_NAME" , names [ "sample" ] ) , ( "PLATFORM_UNIT" , names [ "pu" ] ) , ( "PLATFORM" , names [ "pl" ] ) , ( "TMP_DIR" , tmp_dir ) , ( "OUTPUT" , tx_out_bam ) , ( "SORT_ORDER" , order ) ] if fastq_two : opts . append ( ( "FASTQ2" , fastq_two ) ) picard . run ( "FastqToSam" , opts ) return out_bam
Convert fastq file(s) to BAM, adding sample, run group and platform information.