Run Picard's FixMateInformation generating an aligned output file.

def picard_fixmate(picard, align_bam):
    """Run Picard's FixMateInformation generating an aligned output file.
    """
    base, ext = os.path.splitext(align_bam)
    out_file = "%s-sort%s" % (base, ext)
    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", align_bam),
                        ("OUTPUT", tx_out_file),
                        ("TMP_DIR", tmp_dir),
                        ("SORT_ORDER", "coordinate")]
                picard.run("FixMateInformation", opts)
    return out_file