final SAMSequenceRecord sequence = cramHeader.getSamFileHeader() .getSequence(container.sequenceId); refs = referenceSource.getReferenceBases(sequence, true); if (refs == null) { throw new CRAMException(String.format("Contig %s not found in the reference file.", sequence.getSequenceName())); final SAMSequenceRecord sequence = cramHeader.getSamFileHeader() .getSequence(cramRecord.sequenceId); refs = referenceSource.getReferenceBases(sequence, true);
final SAMSequenceRecord sequence = cramHeader.getSamFileHeader() .getSequence(container.sequenceId); refs = referenceSource.getReferenceBases(sequence, true); if (refs == null) { throw new CRAMException(String.format("Contig %s not found in the reference file.", sequence.getSequenceName())); final SAMSequenceRecord sequence = cramHeader.getSamFileHeader() .getSequence(cramRecord.sequenceId); refs = referenceSource.getReferenceBases(sequence, true);
default: final SAMSequenceRecord sequence = samFileHeader.getSequence(refSeqIndex); refs = source.getReferenceBases(sequence, true); refSeqName = sequence.getSequenceName(); break; if (samRecord.getReferenceIndex() != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && refSeqIndex != samRecord.getReferenceIndex()) { sam2CramRecordFactory.setRefBases(source.getReferenceBases(samFileHeader.getSequence(samRecord.getReferenceIndex()), true));
default: final SAMSequenceRecord sequence = samFileHeader.getSequence(refSeqIndex); refs = source.getReferenceBases(sequence, true); refSeqName = sequence.getSequenceName(); break; if (samRecord.getReferenceIndex() != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && refSeqIndex != samRecord.getReferenceIndex()) { sam2CramRecordFactory.setRefBases(source.getReferenceBases(samFileHeader.getSequence(samRecord.getReferenceIndex()), true));
refBasesFromMixedCaseSource = referenceSourceMixedCase.getReferenceBases(samFileHeader.getSequence(0), true);
refBases = referenceSource.getReferenceBases( header.getSequence(record.sequenceId), true);
refBases = referenceSource.getReferenceBases( header.getSequence(record.sequenceId), true);
refBases = referenceSource.getReferenceBases(header.getSequence(record.sequenceId), true);