final long startOfLastLinearBin = getIndex().getStartOfLastLinearBin(); if (startOfLastLinearBin != -1) { mCompressedInputStream.seek(startOfLastLinearBin);
final long startOfLastLinearBin = getIndex().getStartOfLastLinearBin(); if (startOfLastLinearBin != -1) { mCompressedInputStream.seek(startOfLastLinearBin);
final long startOfLastLinearBin = getIndex().getStartOfLastLinearBin(); if (startOfLastLinearBin != -1) { mCompressedInputStream.seek(startOfLastLinearBin);
final long startOfLastLinearBin = getIndex().getStartOfLastLinearBin(); if (startOfLastLinearBin != -1) { mCompressedInputStream.seek(startOfLastLinearBin);
long startOfLastLinearBin = idx.getStartOfLastLinearBin(); long noCoordinateCount = ((AbstractBAMFileIndex) idx).getNoCoordinateCount(); if (startOfLastLinearBin != -1 && noCoordinateCount > 0) {
long startOfLastLinearBin = idx.getStartOfLastLinearBin(); long noCoordinateCount = ((AbstractBAMFileIndex) idx).getNoCoordinateCount(); if (startOfLastLinearBin != -1 && noCoordinateCount > 0) {
@Override public CloseableIterator<SAMRecord> queryUnmapped() { final long startOfLastLinearBin = getIndex().getStartOfLastLinearBin(); final SeekableStream seekableStream = getSeekableStreamOrFailWithRTE(); final CRAMIterator newIterator; try { seekableStream.seek(0); newIterator = new CRAMIterator(seekableStream, referenceSource, validationStringency); seekableStream.seek(startOfLastLinearBin >>> 16); final Container container = ContainerIO.readContainerHeader(newIterator.getCramHeader().getVersion().major, seekableStream); seekableStream.seek(seekableStream.position() + container.containerByteSize); iterator = newIterator; boolean atAlignments; do { atAlignments = iterator.advanceToAlignmentInContainer(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX, SAMRecord.NO_ALIGNMENT_START); } while (!atAlignments && iterator.hasNext()); } catch (final IOException e) { throw new RuntimeEOFException(e); } return iterator; }
@Override public CloseableIterator<SAMRecord> queryUnmapped() { final long startOfLastLinearBin = getIndex().getStartOfLastLinearBin(); final SeekableStream seekableStream = getSeekableStreamOrFailWithRTE(); final CRAMIterator newIterator; try { seekableStream.seek(0); newIterator = new CRAMIterator(seekableStream, referenceSource, validationStringency); seekableStream.seek(startOfLastLinearBin >>> 16); final Container container = ContainerIO.readContainerHeader(newIterator.getCramHeader().getVersion().major, seekableStream); seekableStream.seek(seekableStream.position() + container.containerByteSize); iterator = newIterator; boolean atAlignments; do { atAlignments = iterator.advanceToAlignmentInContainer(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX, SAMRecord.NO_ALIGNMENT_START); } while (!atAlignments && iterator.hasNext()); } catch (final IOException e) { throw new RuntimeEOFException(e); } return iterator; }