diff --git a/src/main/java/picard/vcf/GenotypeConcordance.java b/src/main/java/picard/vcf/GenotypeConcordance.java index 9f9ae1a2a..185fcce58 100644 --- a/src/main/java/picard/vcf/GenotypeConcordance.java +++ b/src/main/java/picard/vcf/GenotypeConcordance.java @@ -160,9 +160,10 @@ private final Log log = Log.getInstance(GenotypeConcordance.class); private final ProgressLogger progress = new ProgressLogger(log, 10000, "checked", "variants"); - public static final String SUMMARY_METRICS_FILE_EXTENSION = ".genotype_concordance_summary_metrics"; - public static final String DETAILED_METRICS_FILE_EXTENSION = ".genotype_concordance_detail_metrics"; + public static final String SUMMARY_METRICS_FILE_EXTENSION = ".genotype_concordance_summary_metrics"; + public static final String DETAILED_METRICS_FILE_EXTENSION = ".genotype_concordance_detail_metrics"; public static final String CONTINGENCY_METRICS_FILE_EXTENSION = ".genotype_concordance_contingency_metrics"; + public static final String OUTPUT_VCF_FILE_EXTENSION = ".genotype_concordance.vcf.gz"; protected GenotypeConcordanceCounts snpCounter; public GenotypeConcordanceCounts getSnpCounter() { return snpCounter; } @@ -381,7 +382,7 @@ private boolean indexExists(final File vcf) { /** Gets the variant context writer if the output VCF is to be written, otherwise empty. */ private Optional getVariantContextWriter(final VCFFileReader truthReader, final VCFFileReader callReader) { if (OUTPUT_VCF) { - final File outputVcfFile = new File(OUTPUT + ".vcf.gz"); + final File outputVcfFile = new File(OUTPUT + OUTPUT_VCF_FILE_EXTENSION); final VariantContextWriterBuilder builder = new VariantContextWriterBuilder() .setOutputFile(outputVcfFile) .setReferenceDictionary(callReader.getFileHeader().getSequenceDictionary()) diff --git a/src/test/java/picard/vcf/GenotypeConcordanceTest.java b/src/test/java/picard/vcf/GenotypeConcordanceTest.java index 34214e2f5..5cc37731f 100644 --- a/src/test/java/picard/vcf/GenotypeConcordanceTest.java +++ b/src/test/java/picard/vcf/GenotypeConcordanceTest.java @@ -131,7 +131,7 @@ public void testGenotypeConcordance(final File vcf1, final String sample1, final final File outputSummaryFile = new File(outputBaseFileName.getAbsolutePath() + GenotypeConcordance.SUMMARY_METRICS_FILE_EXTENSION); final File outputDetailsFile = new File(outputBaseFileName.getAbsolutePath() + GenotypeConcordance.DETAILED_METRICS_FILE_EXTENSION); final File outputContingencyFile = new File(outputBaseFileName.getAbsolutePath() + GenotypeConcordance.CONTINGENCY_METRICS_FILE_EXTENSION); - final Path outputVcfFile = Paths.get(outputBaseFileName.getAbsolutePath() + ".vcf.gz"); + final Path outputVcfFile = Paths.get(outputBaseFileName.getAbsolutePath() + GenotypeConcordance.OUTPUT_VCF_FILE_EXTENSION); outputSummaryFile.deleteOnExit(); outputDetailsFile.deleteOnExit(); outputContingencyFile.deleteOnExit();