From 12269d8608daad59257e2ffa9231c70674d4b517 Mon Sep 17 00:00:00 2001 From: tfenne Date: Mon, 9 Jan 2017 15:10:24 -0500 Subject: [PATCH 1/2] Added '.genotype_concordance' into the output VCF name. --- src/main/java/picard/vcf/GenotypeConcordance.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/picard/vcf/GenotypeConcordance.java b/src/main/java/picard/vcf/GenotypeConcordance.java index 9f9ae1a2a..76ec7b72a 100644 --- a/src/main/java/picard/vcf/GenotypeConcordance.java +++ b/src/main/java/picard/vcf/GenotypeConcordance.java @@ -381,7 +381,7 @@ 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 + ".genotype_concordance.vcf.gz"); final VariantContextWriterBuilder builder = new VariantContextWriterBuilder() .setOutputFile(outputVcfFile) .setReferenceDictionary(callReader.getFileHeader().getSequenceDictionary()) From 5870c17bb8f9c333c9bdab47b9e5fd5f04d1aa41 Mon Sep 17 00:00:00 2001 From: tfenne Date: Mon, 9 Jan 2017 16:47:25 -0500 Subject: [PATCH 2/2] Fix tests and review feedback. --- src/main/java/picard/vcf/GenotypeConcordance.java | 7 ++++--- src/test/java/picard/vcf/GenotypeConcordanceTest.java | 2 +- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/src/main/java/picard/vcf/GenotypeConcordance.java b/src/main/java/picard/vcf/GenotypeConcordance.java index 76ec7b72a..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 + ".genotype_concordance.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();