/** * Should we also write a BCF file alongside our VCF file for testing * * TODO -- remove me when argument generateShadowBCF is removed * * @return */ public boolean alsoWriteBCFForTest() { return engine.getArguments().numberOfDataThreads == 1 && // only works single threaded ! isCompressed() && // for non-compressed outputs getOutputFile() != null && // that are going to disk engine.getArguments().generateShadowBCF; // and we actually want to do it }
if ( allowCompressed && stub.isCompressed() ) stream = new BlockCompressedOutputStream(file); else final VariantContextWriterBuilder.OutputType fileOutputType = allowCompressed && stub.isCompressed() ? VariantContextWriterBuilder.OutputType.BLOCK_COMPRESSED_VCF : VariantContextWriterBuilder.OutputType.VCF; final EnumSet<Options> options = stub.getWriterOptions(indexOnTheFly);