/** attempt to close the VCF file */
public void close() {
try {
// close the underlying output stream
outputStream.close();
// close the index stream (keep it separate to help debugging efforts)
if (indexer != null) {
final Index index = indexer.finalizeIndex(positionalOutputStream.getPosition());
setIndexSequenceDictionary(index, refDict);
index.write(idxStream);
idxStream.close();
}
} catch (IOException e) {
throw new RuntimeException("Unable to close index for " + getStreamName(), e);
}
}
/**
* add a record to the file
*
* @param vc the Variant Context object
*/
public void add(final VariantContext vc) {
// if we are doing on the fly indexing, add the record ***before*** we write any bytes
if (indexer != null) indexer.addFeature(vc, positionalOutputStream.getPosition());
}