INNER CODE UNIT · Python

proc_chr

nloyfer/wgbs_tools · src/python/add_cpg_counts.py:31

def proc_chr(input_path, out_path_name, region, genome, paired_end, ex_flags, mapq,
             debug, verbose, min_cpg, clip, bed_file, extended_bed, add_pat, in_flags,
             drop_singles):
    """ Convert a temp single chromosome file, extracted from a bam file,
        into a sam formatted (no header) output file."""

    # Run patter tool 'bam' mode on a single chromosome

    unsorted_bam = out_path_name + '_unsorted.output.bam'
    out_path = out_path_name + '.output.bam'
    out_directory = os.path.dirname(out_path)

    # use samtools to extract only the reads from 'chrom'
    # flag = '-f 3' if paired_end else ''
    if in_flags is None:
        in_flags = '-f 3' if paired_end else ''
    else:
        in_flags = f'-f {in_flags}'

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