public void addAlignment(SAMRecord samRecord) { final SAMReaderID id = toolkit.getReaderIDForRead(samRecord); String rg = samRecord.getStringAttribute("RG"); if (rg != null) { String rg_orig = toolkit.getReadsDataSource().getOriginalReadGroupId(rg); samRecord.setAttribute("RG", rg_orig); } addAlignment(samRecord, id); }