INNER CODE UNIT · Python

main

cbg-ethz/V-pipe · workflow/scripts/alignmentBias.py:91

def main():
    args = parse_args()
    reference = SeqIO.read(args.reference_file, "fasta")
    reference_len = len(reference)
    start = None
    end = None

    hap_cnt = {}
    hap_coverage = {}
    with pysam.AlignmentFile(args.bamfile, "rb") as alnfile:
        for read in alnfile.fetch(reference=reference.id, start=start, end=end):
            query_name = read.query_name
            hapID = query_name.split("-")[0]
            if hapID in hap_cnt:
                hap_cnt[hapID] += 1
            else:
                hap_cnt[hapID] = 1

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