/**
* Constructs an object which will write directly into the output file provided by the stub.
* Intentionally delaying the writing of the header -- this should be filled in by the walker.
*
* <p>Respecs the isCompressed() request in stub, so if isCompressed() is true then this will
* create a storage output that dumps output to a BlockCompressedOutputStream.
*
* @param stub Stub to use when constructing the output file.
*/
public VariantContextWriterStorage(VariantContextWriterStub stub) {
if (stub.getOutputFile() != null) {
this.file = stub.getOutputFile();
writer = vcfWriterToFile(stub, stub.getOutputFile(), true, true);
} else if (stub.getOutputStream() != null) {
this.file = null;
this.stream = stub.getOutputStream();
writer =
VariantContextWriterFactory.create(
stream, stub.getMasterSequenceDictionary(), stub.getWriterOptions(false));
} else
throw new ReviewedStingException(
"Unable to create target to which to write; storage was provided with neither a file nor a stream.");
}
