INNER CODE UNIT · Python

percent_aligned

cbg-ethz/V-pipe · workflow/scripts/alignmentBias.py:113

            percent_aligned = read.query_alignment_length / read.infer_read_length()
            assert percent_aligned <= 1, f"{cigar_arr}"
            if hapID in hap_coverage:
                hap_coverage[hapID] += percent_aligned
            else:
                hap_coverage[hapID] = percent_aligned

    for k, v in hap_cnt.items():
        aux = hap_coverage[k] / v
        assert aux <= 1, f"{aux}"
        hap_coverage[k] = aux

    # Parse FASTQ file to compute the expected number of reads per haplotype
    hap_expected = {}
    total = 0
    for read in SeqIO.parse(args.fastq_file, "fastq"):
        total += 1
        hapID = read.id.split("-")[0]

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