public void validateOutputBCFIfPossible(final String name, final File resultFile) { final File bcfFile = BCF2Utils.shadowBCF(resultFile); if ( bcfFile != null && bcfFile.exists() ) { logger.warn("Checking shadow BCF output file " + bcfFile + " against VCF file " + resultFile); try { assertVCFandBCFFilesAreTheSame(resultFile, bcfFile); logger.warn(" Shadow BCF PASSED!"); } catch ( Exception e ) { Assert.fail("Exception received reading shadow BCFFile " + bcfFile + " for test " + name, e); } } }
final File potentalShadowBCFFile = BCF2Utils.shadowBCF(fl); potentalShadowBCFFile.deleteOnExit(); new File(potentalShadowBCFFile.getAbsolutePath() + Tribble.STANDARD_INDEX_EXTENSION).deleteOnExit();
! ( options.contains(Options.FORCE_BCF) || file != null && (file.getName().endsWith(".bcf") || file.getName().endsWith(".bcf.gz")) ) ) { final File bcfFile = BCF2Utils.shadowBCF(file); if ( bcfFile != null ) { final VariantContextWriter bcfWriter = new VariantContextWriterBuilder()