Convert BAM to bed file using BEDTools.

def convert_bam_to_bed(in_bam, out_file):
    """Convert BAM to bed file using BEDTools.
    """
    with file_transaction(out_file) as tx_out_file:
        with open(tx_out_file, "w") as out_handle:
            subprocess.check_call(["bamToBed", "-i", in_bam, "-tag", "NM"],
                                  stdout=out_handle)
    return out_file