this.recordRangeInfo = recordRangeInfo; long readStart = chunk.getChunkStart() - recordRangeInfo.getTotalReferencesLength(); if (readStart < 0) { readStart = 0; long readEnd = chunk.getChunkEnd() - recordRangeInfo.getTotalReferencesLength(); if (readEnd > recordRangeInfo.getNumberOfReads()) { readEnd = recordRangeInfo.getNumberOfReads();
this.recordRangeInfo = recordRangeInfo; long readStart = chunk.getChunkStart() - recordRangeInfo.getTotalReferencesLength(); if (readStart < 0) { readStart = 0; long readEnd = chunk.getChunkEnd() - recordRangeInfo.getTotalReferencesLength(); if (readEnd > recordRangeInfo.getNumberOfReads()) { readEnd = recordRangeInfo.getNumberOfReads();
@Override public CloseableIterator<SAMRecord> queryUnmapped() { if (recordRangeInfo.getTotalRecordRangeLength() <= 0) { throw new RuntimeException("Cannot create file span - SRA file is empty"); } SAMFileSpan span = new BAMFileSpan(new Chunk(recordRangeInfo.getTotalReferencesLength(), recordRangeInfo.getTotalRecordRangeLength())); return getIterator(span); }
while (currentChunk != null) { if (alignmentIterator == null) { if (currentChunk.getChunkStart() < recordRangeInfo.getTotalReferencesLength()) { alignmentIterator = new SRAAlignmentIterator(accession, run, header, cachedReferences, recordRangeInfo, currentChunk); if (validationStringency != null) { if (currentChunk.getChunkEnd() > recordRangeInfo.getTotalReferencesLength()) { unalignmentIterator = new SRAUnalignmentIterator(accession, run, header, recordRangeInfo, currentChunk); if (validationStringency != null) {
while (currentChunk != null) { if (alignmentIterator == null) { if (currentChunk.getChunkStart() < recordRangeInfo.getTotalReferencesLength()) { alignmentIterator = new SRAAlignmentIterator(accession, run, header, cachedReferences, recordRangeInfo, currentChunk); if (validationStringency != null) { if (currentChunk.getChunkEnd() > recordRangeInfo.getTotalReferencesLength()) { unalignmentIterator = new SRAUnalignmentIterator(accession, run, header, recordRangeInfo, currentChunk); if (validationStringency != null) {
@Override public CloseableIterator<SAMRecord> queryUnmapped() { if (recordRangeInfo.getTotalRecordRangeLength() <= 0) { throw new RuntimeException("Cannot create file span - SRA file is empty"); } SAMFileSpan span = new BAMFileSpan(new Chunk(recordRangeInfo.getTotalReferencesLength(), recordRangeInfo.getTotalRecordRangeLength())); return getIterator(span); }