/** * Constructs an object which will redirect into a different file. * * Note that this function does not respect the isCompressed() request from the stub, in order * to ensure that tmp. files can be read back in by the Tribble system, and merged with the mergeInto function. * * @param stub Stub to use when synthesizing file / header info. * @param tempFile File into which to direct the output data. */ public VariantContextWriterStorage(VariantContextWriterStub stub, File tempFile) { //logger.debug("Creating temporary output file " + tempFile.getAbsolutePath() + " for VariantContext output."); this.file = tempFile; this.writer = vcfWriterToFile(stub, file, false, false); writer.writeHeader(stub.getVCFHeader()); }