final int binNum = computeIndexingBin(slice);
final int binNum = computeIndexingBin(slice);
/** * Create a CRAM indexer that writes BAI to a file. * * @param output binary BAM Index (.bai) file * @param fileHeader header for the corresponding bam file */ public CRAMBAIIndexer(final File output, final SAMFileHeader fileHeader) { numReferences = fileHeader.getSequenceDictionary().size(); indexBuilder = new BAMIndexBuilder(fileHeader); outputWriter = new BinaryBAMIndexWriter(numReferences, output); }
/** * Create a CRAM indexer that writes BAI to a stream. * * @param output Index will be written here. output will be closed when finish() method is called. * @param fileHeader header for the corresponding bam file. */ public CRAMBAIIndexer(final OutputStream output, final SAMFileHeader fileHeader) { numReferences = fileHeader.getSequenceDictionary().size(); indexBuilder = new BAMIndexBuilder(fileHeader); outputWriter = new BinaryBAMIndexWriter(numReferences, output); }
/** * After all the slices have been processed, finish is called. * Writes any final information and closes the output file. */ public void finish() { // process any remaining references advanceToReference(numReferences); outputWriter.writeNoCoordinateRecordCount(indexBuilder.getNoCoordinateRecordCount()); outputWriter.close(); }
/** * Create a CRAM indexer that writes BAI to a stream. * * @param output Index will be written here. output will be closed when finish() method is called. * @param fileHeader header for the corresponding bam file. */ public CRAMBAIIndexer(final OutputStream output, final SAMFileHeader fileHeader) { numReferences = fileHeader.getSequenceDictionary().size(); indexBuilder = new BAMIndexBuilder(fileHeader); outputWriter = new BinaryBAMIndexWriter(numReferences, output); }
/** * write out any references between the currentReference and the nextReference */ private void advanceToReference(final int nextReference) { while (currentReference < nextReference) { final BAMIndexContent content = indexBuilder.processReference(currentReference); outputWriter.writeReference(content); currentReference++; indexBuilder.startNewReference(); } }
/** * Create a CRAM indexer that writes BAI to a file. * * @param output binary BAM Index (.bai) file * @param fileHeader header for the corresponding bam file */ public CRAMBAIIndexer(final File output, final SAMFileHeader fileHeader) { numReferences = fileHeader.getSequenceDictionary().size(); indexBuilder = new BAMIndexBuilder(fileHeader); outputWriter = new BinaryBAMIndexWriter(numReferences, output); }
/** * write out any references between the currentReference and the nextReference */ private void advanceToReference(final int nextReference) { while (currentReference < nextReference) { final BAMIndexContent content = indexBuilder.processReference(currentReference); outputWriter.writeReference(content); currentReference++; indexBuilder.startNewReference(); } }
/** * After all the slices have been processed, finish is called. * Writes any final information and closes the output file. */ public void finish() { // process any remaining references advanceToReference(numReferences); outputWriter.writeNoCoordinateRecordCount(indexBuilder.getNoCoordinateRecordCount()); outputWriter.close(); }