chimeric.py 文件源码

def chimeric_reads(bamfile, virus_contig, duplicates):
    igv_chimeric_file = os.path.splitext(args.bamfile)[0] + ".chimeric.igv.bam"
    if os.path.exists(igv_chimeric_file):
        return igv_chimeric_file
    with pysam.Samfile(args.bamfile, "rb") as in_handle, \
         pysam.Samfile(igv_chimeric_file, "wb", template=in_handle) as out_handle:
        for read in in_handle:
            try:
                chrom = in_handle.getrname(read.tid)
            except ValueError:
                continue
            if not is_chimeric_read(read, chrom, virus_contig):
                continue
            if read.qname in duplicates:
                continue
            out_handle.write(read)
    return igv_chimeric_file