public BAMShardIndexer(OutputStream output, SAMFileHeader header, int reference) { indexBuilder = new BAMIndexBuilder(header.getSequenceDictionary(), reference); final boolean isFirstIndexShard = reference == 0; final int numReferencesToWriteInTheHeader = isFirstIndexShard ? header.getSequenceDictionary().size() : 0; outputWriter = new BinaryBAMShardIndexWriter(numReferencesToWriteInTheHeader, output); this.referenceIndex = reference; }
public BAMShardIndexer(OutputStream output, SAMFileHeader header, int reference) { indexBuilder = new BAMIndexBuilder(header.getSequenceDictionary(), reference); final boolean isFirstIndexShard = reference == 0; final int numReferencesToWriteInTheHeader = isFirstIndexShard ? header.getSequenceDictionary().size() : 0; outputWriter = new BinaryBAMShardIndexWriter(numReferencesToWriteInTheHeader, output); this.referenceIndex = reference; }