bam.py 文件源码

def concatenate(out_file_name, all_in_file_names):
    """ Concatenate a list of bam files into a final output file """

    # Filter out empty BAM files -- these cause samtools cat to generate
    # a BAM with a premature end block
    in_file_names = [f for f in all_in_file_names if not bam_is_empty(f)]

    if len(in_file_names) > 1:
        args = ['samtools', 'cat', '-o', out_file_name]
        args.extend(in_file_names)
        subprocess.check_call(args)
    elif len(in_file_names) == 0:
        # If all the BAMs are empty, just copy 1 over
        shutil.copy(all_in_file_names[0], out_file_name)
    else:
        shutil.copy(in_file_names[0], out_file_name)