Add read group information to BAM files and coordinate sort.

def picard_fix_rgs(picard, in_bam, names):
    """Add read group information to BAM files and coordinate sort.
    """
    out_file = "%s-fixrgs.bam" % os.path.splitext(in_bam)[0]
    if not file_exists(out_file):
        with tx_tmpdir(picard._config) as tmp_dir:
            with file_transaction(picard._config, out_file) as tx_out_file:
                opts = [("INPUT", in_bam),
                        ("OUTPUT", tx_out_file),
                        ("SORT_ORDER", "coordinate"),
                        ("RGID", names["rg"]),
                        ("RGLB", names.get("lb", "unknown")),
                        ("RGPL", names["pl"]),
                        ("RGPU", names["pu"]),
                        ("RGSM", names["sample"]),
                        ("TMP_DIR", tmp_dir)]
                picard.run("AddOrReplaceReadGroups", opts)
    return out_file