sample_info.py 文件源码

def get_bam_coverages(options, sample, dataset):
    window_skip = int(1e6)
    window_size = 1000
    skip_at_ends = int(1e6)

    bam = pysam.AlignmentFile(dataset.bam)

    print "getting coverages"
    coverages = []
    count = 0
    for chrom, start, end in get_search_regions(options.reference, 
                                                window_skip, window_size, skip_at_ends):
        coverages.append(bam.count(chrom, start, end))

        if count % 1000 == 0:
            print count
        count += 1
    return coverages