/** * The following passage is for paranoid mode only. When java is run with * asserts on it will throw an {@link AssertionError} if read bases or * quality scores of a restored SAM record mismatch the original. This is * effectively a runtime round trip test. */ private static void assertSame(SAMFileHeader samFileHeader, List<SAMRecord> samRecords, List<CramCompressionRecord> cramRecords) { @SuppressWarnings("UnusedAssignment") boolean assertsEnabled = false; assert assertsEnabled = true; if (assertsEnabled) { final Cram2SamRecordFactory f = new Cram2SamRecordFactory(samFileHeader); for (int i = 0; i < samRecords.size(); i++) { final SAMRecord restoredSamRecord = f.create(cramRecords.get(i)); assert (restoredSamRecord.getAlignmentStart() == samRecords.get(i).getAlignmentStart()); assert (restoredSamRecord.getReferenceName().equals(samRecords.get(i).getReferenceName())); assert (restoredSamRecord.getReadString().equals(samRecords.get(i).getReadString())); assert (restoredSamRecord.getBaseQualityString().equals(samRecords.get(i).getBaseQualityString())); } } }
codec.setOutputStream(os); for (CramCompressionRecord record : records) { SAMRecord samRecord = f.create(record); codec.encode(samRecord);
CramToBam_OBA_Function(CramHeader header, ReferenceSource referenceSource) { this.header = header; parser = new ContainerParser(header.getSamFileHeader()); f = new Cram2SamRecordFactory(header.getSamFileHeader()); codec = new BAMRecordCodec(header.getSamFileHeader()); n = new CramNormalizer(header.getSamFileHeader(), referenceSource); log.info("converter created"); }
container.header.substitutionMatrix); final Cram2SamRecordFactory cramToSamRecordFactory = new Cram2SamRecordFactory( cramHeader.getSamFileHeader()); final SAMRecord samRecord = cramToSamRecordFactory.create(cramRecord); if (!cramRecord.isSegmentUnmapped()) { final SAMSequenceRecord sequence = cramHeader.getSamFileHeader()
container.header.substitutionMatrix); final Cram2SamRecordFactory cramToSamRecordFactory = new Cram2SamRecordFactory( cramHeader.getSamFileHeader()); final SAMRecord samRecord = cramToSamRecordFactory.create(cramRecord); if (!cramRecord.isSegmentUnmapped()) { final SAMSequenceRecord sequence = cramHeader.getSamFileHeader()
normTime += time2 - time1; Cram2SamRecordFactory c2sFactory = new Cram2SamRecordFactory(cramHeader.getSamFileHeader()); SAMRecord s = c2sFactory.create(r);
final Cram2SamRecordFactory f = new Cram2SamRecordFactory(samFileHeader); for (int i = 0; i < samRecords.size(); i++) { final SAMRecord restoredSamRecord = f.create(cramRecords.get(i)); assert (restoredSamRecord.getAlignmentStart() == samRecords.get(i).getAlignmentStart()); assert (restoredSamRecord.getReferenceName().equals(samRecords.get(i).getReferenceName()));
final Cram2SamRecordFactory f = new Cram2SamRecordFactory(samFileHeader); for (int i = 0; i < samRecords.size(); i++) { final SAMRecord restoredSamRecord = f.create(cramRecords.get(i)); assert (restoredSamRecord.getAlignmentStart() == samRecords.get(i).getAlignmentStart()); assert (restoredSamRecord.getReferenceName().equals(samRecords.get(i).getReferenceName()));