diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index ed5d2360f..3719dceb2 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -46,7 +46,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils; public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation { private final static boolean DEBUG = false; - private final static int MIN_CONTEXT_WING_SIZE = 20; + private final static int MIN_CONTEXT_WING_SIZE = 10; private final static int MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER = 50; private final static char REGEXP_WILDCARD = '.'; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java index d0d0cd6ef..7046da8ea 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java @@ -18,7 +18,7 @@ import java.util.List; import java.util.Arrays; -public class QualByDepth implements InfoFieldAnnotation, StandardAnnotation { +public class QualByDepth extends AnnotationByDepth implements InfoFieldAnnotation, StandardAnnotation { public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) @@ -55,13 +55,18 @@ public class QualByDepth implements InfoFieldAnnotation, StandardAnnotation { if ( qual == 0.0 ) qual = 10.0 * vc.getNegLog10PError(); - double QbyD = qual / (double)depth; + double sumGLbyD = qual / (double)depth; + + int qDepth = annotationByVariantDepth(genotypes, stratifiedContexts); + double QD = 10.0 * vc.getNegLog10PError() / (double)qDepth; + Map map = new HashMap(); - map.put(getKeyNames().get(0), String.format("%.2f", QbyD)); + map.put(getKeyNames().get(0), String.format("%.2f", QD)); + map.put(getKeyNames().get(1), String.format("%.2f", sumGLbyD)); return map; } - public List getKeyNames() { return Arrays.asList("QD"); } + public List getKeyNames() { return Arrays.asList("QD", "sumGLbyD"); } public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Variant Confidence/Quality by Depth")); } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java index 9818e6058..83aec2b93 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java @@ -84,7 +84,7 @@ public class GenerateVariantClustersWalker extends RodWalker 0 ) { - if(alignment[alignPos-1] == (byte) 'A') { - alignment[alignPos-1] = PileupElement.INSERTION_BASE_A; - } else if(alignment[alignPos-1] == (byte) 'C') { - alignment[alignPos-1] = PileupElement.INSERTION_BASE_C; - } else if(alignment[alignPos-1] == (byte) 'T') { - alignment[alignPos-1] = PileupElement.INSERTION_BASE_T; - } else if(alignment[alignPos-1] == (byte) 'G') { - alignment[alignPos-1] = PileupElement.INSERTION_BASE_G; - } - } case S: for ( int jjj = 0; jjj < elementLength; jjj++ ) { readPos++; 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 6545128e0..cfebe7dd2 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -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("98861116ac1cdaf152adead3183664d8")); + Arrays.asList("c62ee353f7ddafa2348b461d9e107f2f")); 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("53d083505fc82fb388566d3856ed20ba")); + Arrays.asList("0c43cfb9b08f63f49396e3bf8b3d843f")); executeTest("test file has annotations, 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("c5807c5794c3a847d78e3800553d989a")); + Arrays.asList("3aa1415f7bc6d41c4f14343187377f96")); 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("a9b2a7adee7ba8b0f5d7ff8d92e6dfbd")); + Arrays.asList("bf3bc299552b595f791486a1f8dbc509")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } @@ -79,7 +79,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testOverwritingHeader() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1, - Arrays.asList("e3c839910aa82061742e33196b112cb0")); + Arrays.asList("28829de1afd9dcb41ed666f949c4f5cc")); executeTest("test overwriting header", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index dba3eb8fe..54fec9cb0 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -25,7 +25,7 @@ public class public void testMultiSamplePilot1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1, - Arrays.asList("ae901e034b00aef16d36295821b3ea63")); + Arrays.asList("6c04cc01cf6bebe4bdbc025fd45c5559")); executeTest("testMultiSamplePilot1", spec); } @@ -33,7 +33,7 @@ public class public void testMultiSamplePilot2() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1, - Arrays.asList("2ad026dee3fe592c124eb8724a843a5e")); + Arrays.asList("84efe068164891dbec7c85ff6cc33df3")); executeTest("testMultiSamplePilot2", spec); } @@ -41,7 +41,7 @@ public class public void testSingleSamplePilot2() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1, - Arrays.asList("bc573090407ae9ec4401757eaa03de20")); + Arrays.asList("c7decebadb35067a38b9be3c43c1fb76")); executeTest("testSingleSamplePilot2", spec); } @@ -51,7 +51,7 @@ public class // // -------------------------------------------------------------------------------------------------------------- - private final static String COMPRESSED_OUTPUT_MD5 = "1889ecc5aa1b23b2e77b1bd192577f1a"; + private final static String COMPRESSED_OUTPUT_MD5 = "66bcb3f7b20d4fbe7849b616bfe69c0f"; @Test public void testCompressedOutput() { @@ -78,7 +78,7 @@ public class @Test public void testParallelization() { - String md5 = "d19745ab31f903de8d5a8e853b4e52dd"; + String md5 = "a0032a9952c94a55e0fa42e2dec33169"; WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1, @@ -105,12 +105,12 @@ public class @Test public void testParameter() { HashMap e = new HashMap(); - e.put( "-genotype", "37d3954e19309a24c386758afad93252" ); - e.put( "-all_bases", "04568093c5dc70fa7965b4ab15fd0f7e" ); - e.put( "--min_base_quality_score 26", "5d1886a9637183707645bc2dc6bf8282" ); - e.put( "--min_mapping_quality_score 26", "78423524cf56cce1d0847847d542459f" ); - e.put( "--max_mismatches_in_40bp_window 5", "2963c771aafe84b62082f475d20bad5e" ); - e.put( "--p_nonref_model GRID_SEARCH", "c254a4e593b4ffb112299be874503ce0" ); + e.put( "-genotype", "4a623d4a68fba4f9f8d7e915af0cc450" ); + e.put( "-all_bases", "2ab5106795c70a63d8dd2353ee0f1427" ); + e.put( "--min_base_quality_score 26", "9c9be22923b9ba0d588f3d37385ae4b0" ); + e.put( "--min_mapping_quality_score 26", "aa36bb2f4fc5bd6b6c4206e0a084a577" ); + e.put( "--max_mismatches_in_40bp_window 5", "4914ed25a8ca22c7aea983999cd6768a" ); + e.put( "--p_nonref_model GRID_SEARCH", "dd4fb1fb304e44b82c9cc3d4cc257172" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -124,12 +124,12 @@ public class public void testConfidence() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1, - Arrays.asList("c254a4e593b4ffb112299be874503ce0")); + Arrays.asList("dd4fb1fb304e44b82c9cc3d4cc257172")); executeTest("testConfidence1", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1, - Arrays.asList("d2323a0234d27257393f4931fca70dbc")); + Arrays.asList("eef4e314d0cdae669454232ffbbab8ea")); executeTest("testConfidence2", spec2); } @@ -141,8 +141,8 @@ public class @Test public void testHeterozyosity() { HashMap e = new HashMap(); - e.put( 0.01, "96e85b26cf5f0a523b4b0886dbb902b1" ); - e.put( 1.0 / 1850, "5ffecb68b52169ded04312aa5dcdc137" ); + e.put( 0.01, "1bbd2e24ddec902339eac481565d7f0a" ); + e.put( 1.0 / 1850, "472d2d6c375a7c6d2edb464a12f10742" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -165,7 +165,7 @@ public class " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("e65c95a9d2a0995078d3e6835cf4ee61")); + Arrays.asList("eb4144006eda780d69b6979817ceb58d")); executeTest(String.format("testMultiTechnologies"), spec); }