Retrieve duplicate information from input BAM file.

def _get_current_dup_metrics(self, align_bam):
        """Retrieve duplicate information from input BAM file.
        """
        metrics_file = "%s.dup_metrics" % os.path.splitext(align_bam)[0]
        if not file_exists(metrics_file):
            dups = 0
            with pysam.Samfile(align_bam, "rb") as bam_handle:
                for read in bam_handle:
                    if (read.is_paired and read.is_read1) or not read.is_paired:
                        if read.is_duplicate:
                            dups += 1
            with open(metrics_file, "w") as out_handle:
                out_handle.write("# custom bcbio-nextgen metrics\n")
                out_handle.write("READ_PAIR_DUPLICATES\t%s\n" % dups)
        return metrics_file