@Override public SAMRecord next() { if (!hasNext()) { throw new NoSuchElementException("No more alignments are available"); } return nextUnalignment(); }
@Override public boolean hasNext() { // check unaligned if (hasMoreUnalignedFragments == null) { try { lastRecord.detachFromIterator(); nextUnalignedFragment(); } catch (ErrorMsg e) { throw new RuntimeException(e); } } return hasMoreUnalignedFragments; }
public void setValidationStringency(ValidationStringency validationStringency) { this.validationStringency = validationStringency; if (alignmentIterator != null) { alignmentIterator.setValidationStringency(validationStringency); } if (unalignmentIterator != null) { unalignmentIterator.setValidationStringency(validationStringency); } } }
unalignmentIterator = new SRAUnalignmentIterator(accession, run, header, recordRangeInfo, currentChunk); if (validationStringency != null) { unalignmentIterator.setValidationStringency(validationStringency); if (unalignmentIterator != null && unalignmentIterator.hasNext()) { return true;
/** * Call hasNext to make sure that one of inner iterators points to the next record, the retrieve the record from * one of them. * @return lazy SRA record */ @Override public SAMRecord next() { if (!hasNext()) { throw new NoSuchElementException("No more records are available in SRAIterator"); } if (alignmentIterator != null && alignmentIterator.hasNext()) { return alignmentIterator.next(); } return unalignmentIterator.next(); }
unalignmentIterator = new SRAUnalignmentIterator(accession, run, header, recordRangeInfo, currentChunk); if (validationStringency != null) { unalignmentIterator.setValidationStringency(validationStringency); if (unalignmentIterator != null && unalignmentIterator.hasNext()) { return true;
/** * Call hasNext to make sure that one of inner iterators points to the next record, the retrieve the record from * one of them. * @return lazy SRA record */ @Override public SAMRecord next() { if (!hasNext()) { throw new NoSuchElementException("No more records are available in SRAIterator"); } if (alignmentIterator != null && alignmentIterator.hasNext()) { return alignmentIterator.next(); } return unalignmentIterator.next(); }
@Override public SAMRecord next() { if (!hasNext()) { throw new NoSuchElementException("No more alignments are available"); } return nextUnalignment(); }
@Override public boolean hasNext() { // check unaligned if (hasMoreUnalignedFragments == null) { try { lastRecord.detachFromIterator(); nextUnalignedFragment(); } catch (ErrorMsg e) { throw new RuntimeException(e); } } return hasMoreUnalignedFragments; }
public void setValidationStringency(ValidationStringency validationStringency) { this.validationStringency = validationStringency; if (alignmentIterator != null) { alignmentIterator.setValidationStringency(validationStringency); } if (unalignmentIterator != null) { unalignmentIterator.setValidationStringency(validationStringency); } } }