INNER CODE UNIT · Python

FLAGS_FILTER_NANOPORE

nloyfer/wgbs_tools · src/python/bam2pat.py:28

FLAGS_FILTER_NANOPORE = 3844  # 0x4+0x100+0x200+0x400+0x800 = unmapped, secondary, QC-fail, duplicate, supplementary
MAX_READ_SIZE = 1000 # extend samtools view region by this size

# currently we are missing the far mates
def extend_region(region, by=MAX_READ_SIZE):
    if ':' not in region:
        return region
    chrom, r = region.split(':')
    start, end = map(int, r.split('-'))
    start = max(1, start - by)
    end += by
    return f'{chrom}:{start}-{end}'


def subprocess_wrap(cmd, debug):
    if debug:
        eprint(cmd)
        return

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