From 52c534a8f2bba22972fe32d787cc8a04bd12520c Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 12 Jul 2010 20:18:30 +0000 Subject: [PATCH] Updating to VCF 4.0 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3770 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/refdata/VariantContextAdaptors.java | 4 ++-- .../walkers/annotator/VariantAnnotator.java | 2 +- .../VariantAnnotatorIntegrationTest.java | 20 +++++++++---------- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index 0a59ae593..0c0d757dc 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -177,13 +177,13 @@ public class VariantContextAdaptors { Map fields = new HashMap(); for ( Map.Entry e : vcfG.getFields().entrySet() ) { - // todo -- fixme if we put GQ and GF into key itself + // todo -- fixme if we put GQ and FT into key itself if ( ! e.getKey().equals(VCFConstants.GENOTYPE_QUALITY_KEY) && ! e.getKey().equals(VCFConstants.GENOTYPE_FILTER_KEY) ) fields.put(e.getKey(), e.getValue()); } Set genotypeFilters = new HashSet(); - if ( vcfG.isFiltered() ) // setup the FL genotype filter fields + if ( vcfG.isFiltered() ) // setup the genotype filter fields genotypeFilters.addAll(Arrays.asList(vcfG.getFields().get(VCFConstants.GENOTYPE_FILTER_KEY).split(";"))); double qual = vcfG.isMissingQual() ? VariantContext.NO_NEG_LOG_10PERROR : vcfG.getNegLog10PError(); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 01f6ffe08..2899f630f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -142,7 +142,7 @@ public class VariantAnnotator extends RodWalker { hInfo.add(new VCFHeaderLine("annotatorReference", getToolkit().getArguments().referenceFile.getName())); hInfo.addAll(engine.getVCFAnnotationDescriptions()); - vcfWriter = new VCFWriter(out); + vcfWriter = new VCFWriter(out, true); VCFHeader vcfHeader = new VCFHeader(hInfo, samples); vcfWriter.writeHeader(vcfHeader); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 64565b658..3079083ea 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -15,7 +15,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsNotAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("92369e62b3bade625992bc1741e9367a")); + Arrays.asList("179af890ec44e5460188839b3bd6c563")); executeTest("test file has annotations, not asking for annotations, #1", spec); } @@ -23,7 +23,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsNotAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("1a394cdace4ff7698b603c2252ee9365")); + Arrays.asList("b61609288c0b5b2ea3c1b367f00884e0")); executeTest("test file has annotations, not asking for annotations, #2", spec); } @@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("5a8c9c18da89b052e7f3797cd391bff6")); + Arrays.asList("e9b2ba7aa5fda65424956eadbd1cd4de")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("0c8607c69d761bd058b944d1e98708b6")); + Arrays.asList("07c7997177e8a41a9fad91b4d2dc3e12")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -47,7 +47,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsNotAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("006642aabd41e806d3ea64bf5441f1d2")); + Arrays.asList("a56aaddedf6698c57a5a7b56bd476d97")); executeTest("test file doesn't have annotations, not asking for annotations, #1", spec); } @@ -55,7 +55,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsNotAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("c66ed83d2a981c43546d05120809ed57")); + Arrays.asList("ad77d9aa195d9f13fdf0bb33b39772e1")); executeTest("test file doesn't have annotations, not asking for annotations, #2", spec); } @@ -63,7 +63,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("3b570e13bd0e1cb5750da268178ce656")); + Arrays.asList("b7e863281e781b3c947c7c77c9a8c322")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @@ -71,7 +71,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("42e9c57cd5d266fd7837354fc8495176")); + Arrays.asList("13280e9bbc46d1b261d84f2286ac0627")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } @@ -79,7 +79,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoReads() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, - Arrays.asList("374da32e1b9540bfe8ee6ea5b896babd")); + Arrays.asList("027fc7227d900583546161a12e222c83")); executeTest("not passing it any reads", spec); } @@ -87,7 +87,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTag() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, - Arrays.asList("39a6b268e3edc1eee5f71d77460e448e")); + Arrays.asList("1dc170cf522193a791026f0db77fe938")); executeTest("getting DB tag", spec); } }