final int blockSize = byteBuffer.getInt(0); indexWriter.processRecord(recordStart); InputStreamUtils.skipFully(blockIn, blockSize); } catch (EOFException e) {
final int blockSize = byteBuffer.getInt(0); indexWriter.processRecord(recordStart); InputStreamUtils.skipFully(blockIn, blockSize); } catch (RuntimeEOFException e) {
private void processAlignment(final SBIIndexWriter indexWriter, final SAMRecord rec) { final SAMFileSource source = rec.getFileSource(); if (source == null) { throw new SAMException("No source (virtual file offsets); needed for indexing on BAM Record " + rec); } final BAMFileSpan filePointer = (BAMFileSpan) source.getFilePointer(); indexWriter.processRecord(filePointer.getFirstOffset()); }