private void validateMateFields(final SAMRecord record, final long recordNumber) { if (!record.getReadPairedFlag() || record.isSecondaryOrSupplementary()) { return; } validateMateCigar(record, recordNumber); final PairEndInfo pairEndInfo = pairEndInfoByName.remove(record.getReferenceIndex(), record.getReadName()); if (pairEndInfo == null) { pairEndInfoByName.put(record.getMateReferenceIndex(), record.getReadName(), new PairEndInfo(record, recordNumber)); } else { final List<SAMValidationError> errors = pairEndInfo.validateMates(new PairEndInfo(record, recordNumber), record.getReadName()); for (final SAMValidationError error : errors) { addError(error); } } }
private void validateMateFields(final SAMRecord record, final long recordNumber) { if (!record.getReadPairedFlag() || record.isSecondaryOrSupplementary()) { return; } validateMateCigar(record, recordNumber); if (skipMateValidation) { return; } final PairEndInfo pairEndInfo = pairEndInfoByName.remove(record.getReferenceIndex(), record.getReadName()); if (pairEndInfo == null) { pairEndInfoByName.put(record.getMateReferenceIndex(), record.getReadName(), new PairEndInfo(record, recordNumber)); } else { final List<SAMValidationError> errors = pairEndInfo.validateMates(new PairEndInfo(record, recordNumber), record.getReadName()); for (final SAMValidationError error : errors) { addError(error); } } }
private void validateMateFields(final SAMRecord record, final long recordNumber) { if (!record.getReadPairedFlag() || record.isSecondaryOrSupplementary()) { return; } validateMateCigar(record, recordNumber); if (skipMateValidation) { return; } final PairEndInfo pairEndInfo = pairEndInfoByName.remove(record.getReferenceIndex(), record.getReadName()); if (pairEndInfo == null) { pairEndInfoByName.put(record.getMateReferenceIndex(), record.getReadName(), new PairEndInfo(record, recordNumber)); } else { final List<SAMValidationError> errors = pairEndInfo.validateMates(new PairEndInfo(record, recordNumber), record.getReadName()); for (final SAMValidationError error : errors) { addError(error); } } }