merge_pcr_duplicates.py 文件源码

def bam_reader(bam_file, xs_tag):
    global merge_data
    bam = pysam.AlignmentFile(bam_file, "rb")
    filtered_data = []
    chromosomes = bam.references
    for chrom in chromosomes:
        data = bam.fetch(chrom, multiple_iterators=True)

        for entry in data:
            try:
                chrom_bam = bam.get_reference_name(entry.reference_id)
            except:
                continue
            if (entry.is_unmapped == False and chrom_bam == chrom):
                if xs_tag and entry.has_tag("XS"):
                    continue
                else:
                    filtered_data = get_bam_filter(entry, chrom_bam)
        chromosome_info(filtered_data)
        print_results(merge_data)
        merge_data = []
    bam.close()