void advance() { try { mNextRecord = getNextRecord(); if (mNextRecord != null) { ++this.samRecordIndex; // Because some decoding is done lazily, the record needs to remember the validation stringency. mNextRecord.setValidationStringency(mValidationStringency); if (mValidationStringency != ValidationStringency.SILENT) { final List<SAMValidationError> validationErrors = mNextRecord.isValid(); SAMUtils.processValidationErrors(validationErrors, this.samRecordIndex, BAMFileReader.this.getValidationStringency()); } } if (eagerDecode && mNextRecord != null) { mNextRecord.eagerDecode(); } } catch (final IOException exc) { throw new RuntimeException(exc.getMessage(), exc); } }
void advance() { try { mNextRecord = getNextRecord(); if (mNextRecord != null) { ++this.samRecordIndex; // Because some decoding is done lazily, the record needs to remember the validation stringency. mNextRecord.setValidationStringency(mValidationStringency); if (mValidationStringency != ValidationStringency.SILENT) { final List<SAMValidationError> validationErrors = mNextRecord.isValid(mValidationStringency == ValidationStringency.STRICT); SAMUtils.processValidationErrors(validationErrors, this.samRecordIndex, BAMFileReader.this.getValidationStringency()); } } if (eagerDecode && mNextRecord != null) { mNextRecord.eagerDecode(); } } catch (final IOException exc) { throw new RuntimeIOException(exc.getMessage(), exc); } }
void advance() { try { mNextRecord = getNextRecord(); if (mNextRecord != null) { ++this.samRecordIndex; // Because some decoding is done lazily, the record needs to remember the validation stringency. mNextRecord.setValidationStringency(mValidationStringency); if (mValidationStringency != ValidationStringency.SILENT) { final List<SAMValidationError> validationErrors = mNextRecord.isValid(mValidationStringency == ValidationStringency.STRICT); SAMUtils.processValidationErrors(validationErrors, this.samRecordIndex, BAMFileReader.this.getValidationStringency()); } } if (eagerDecode && mNextRecord != null) { mNextRecord.eagerDecode(); } } catch (final IOException exc) { throw new RuntimeIOException(exc.getMessage(), exc); } }
final List<SAMValidationError> validationErrors = info.record.isValid(mValidationStringency == ValidationStringency.STRICT); SAMUtils.processValidationErrors(validationErrors, info.recordIndex, BAMFileReader.this.getValidationStringency());