private void nextReference() { if (!hasMoreReferences) { throw new NoSuchElementException("Cannot get next reference - already at last one"); } try { alignedIterator = null; hasMoreAlignments = false; hasMoreReferences = referencesChunksIterator.hasNext(); if (!hasMoreReferences) { return; } currentReference++; Chunk refChunk = referencesChunksIterator.next(); if (refChunk == null) { return; } Reference reference = cachedReferences.get(currentReference); alignedIterator = reference.getFilteredAlignmentSlice( refChunk.getChunkStart(), refChunk.getChunkEnd() - refChunk.getChunkStart(), Alignment.all, Alignment.startWithinSlice | Alignment.passDuplicates | Alignment.passFailed, 0); hasMoreAlignments = alignedIterator.nextAlignment(); } catch (ErrorMsg e) { throw new RuntimeException(e); } }
private void nextReference() { if (!hasMoreReferences) { throw new NoSuchElementException("Cannot get next reference - already at last one"); } try { alignedIterator = null; hasMoreAlignments = false; hasMoreReferences = referencesChunksIterator.hasNext(); if (!hasMoreReferences) { return; } currentReference++; Chunk refChunk = referencesChunksIterator.next(); if (refChunk == null) { return; } Reference reference = cachedReferences.get(currentReference); alignedIterator = reference.getFilteredAlignmentSlice( refChunk.getChunkStart(), refChunk.getChunkEnd() - refChunk.getChunkStart(), Alignment.all, Alignment.startWithinSlice | Alignment.passDuplicates | Alignment.passFailed, 0); hasMoreAlignments = alignedIterator.nextAlignment(); } catch (ErrorMsg e) { throw new RuntimeException(e); } }