private static void removeMateInfo(SAMRecord rec) { if (rec.getReadPairedFlag()) { // Remove all information of its mate // flag rec.setProperPairFlag(false); // not paired any more rec.setMateUnmappedFlag(false); rec.setMateNegativeStrandFlag(false); // entries rec.setMateReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX); rec.setMateAlignmentStart(0); rec.setInferredInsertSize(0); // TODO: remove tags and values that are mate pair inclined. } }