/** * Finalizes writing and closes the file. * @return count of records with no coordinates. */ public long finish() { final BAMIndexContent content = indexBuilder.processReference(referenceIndex); outputWriter.writeReference(content); outputWriter.close(); return indexBuilder.getNoCoordinateRecordCount(); }
/** * @param nRef Number of reference sequences. If zero is passed then header is not written. * This is useful in sharded writing as we only want the header written for the first shard. * * @param output BAM index output stream. This stream will be closed when BinaryBAMIndexWriter.close() is called. */ public BinaryBAMShardIndexWriter(final int nRef, final OutputStream output) { try { codec = new BinaryCodec(output); if (nRef > 0) { writeHeader(nRef); } } catch (final Exception e) { throw new SAMException("Exception opening output stream", e); } }
writeNullContent(); return; writeNullContent(); return; if (bin.getBinNumber() == GenomicIndexUtil.MAX_BINS) continue; writeBin(bin); writeChunkMetaData(metaData);
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; }
writeNullContent(); return; writeNullContent(); return; if (bin.getBinNumber() == GenomicIndexUtil.MAX_BINS) continue; writeBin(bin); writeChunkMetaData(metaData);
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; }
/** * Finalizes writing and closes the file. * @return count of records with no coordinates. */ public long finish() { final BAMIndexContent content = indexBuilder.processReference(referenceIndex); outputWriter.writeReference(content); outputWriter.close(); return indexBuilder.getNoCoordinateRecordCount(); }
/** * @param nRef Number of reference sequences. If zero is passed then header is not written. * This is useful in sharded writing as we only want the header written for the first shard. * * @param output BAM index output stream. This stream will be closed when BinaryBAMIndexWriter.close() is called. */ public BinaryBAMShardIndexWriter(final int nRef, final OutputStream output) { try { codec = new BinaryCodec(output); if (nRef > 0) { writeHeader(nRef); } } catch (final Exception e) { throw new SAMException("Exception opening output stream", e); } }