bam.py 文件源码

def chrom_counts(self):
        """
        Get read counts per chrom from a bamfile
        """
        self.logger.info(
            "Using index of {} to get read counts per chromosome".format(
                self.filepath))

        analyze_start = time.time()
        samfile = pysam.AlignmentFile(self.filepath, "rb")
        idx_out = samfile.get_index_statistics()
        samfile.close()
        self.logger.info("Index analysis complete. Elapsed time: {} seconds".format(
            time.time() - analyze_start))
        return idx_out