private SAMRecord nextUnalignment() { try { lastRecord = new SRALazyRecord(header, accession, run, unalignedIterator, unalignedIterator.getReadId(), lastUnalignedFragmentIndex); } catch (ErrorMsg e) { throw new RuntimeException(e); } if (validationStringency != null) { lastRecord.setValidationStringency(validationStringency); } hasMoreUnalignedFragments = null; return lastRecord; }
private SAMRecord nextUnalignment() { try { lastRecord = new SRALazyRecord(header, accession, run, unalignedIterator, unalignedIterator.getReadId(), lastUnalignedFragmentIndex); } catch (ErrorMsg e) { throw new RuntimeException(e); } if (validationStringency != null) { lastRecord.setValidationStringency(validationStringency); } hasMoreUnalignedFragments = null; return lastRecord; }
private SAMRecord nextAlignment() { try { lastRecord = new SRALazyRecord(header, accession, run, alignedIterator, alignedIterator.getReadId(), alignedIterator.getAlignmentId()); } catch (ErrorMsg e) { throw new RuntimeException(e); } if (validationStringency != null) { lastRecord.setValidationStringency(validationStringency); } hasMoreAlignments = null; return lastRecord; }
private SAMRecord nextAlignment() { try { lastRecord = new SRALazyRecord(header, accession, run, alignedIterator, alignedIterator.getReadId(), alignedIterator.getAlignmentId()); } catch (ErrorMsg e) { throw new RuntimeException(e); } if (validationStringency != null) { lastRecord.setValidationStringency(validationStringency); } hasMoreAlignments = null; return lastRecord; }