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.
}
}
