diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java index 3d5f088f6..782a321db 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java @@ -12,7 +12,7 @@ import java.util.Arrays; public class BaseQualityRankSumTest extends RankSumTest { public List getKeyNames() { return Arrays.asList("BaseQRankSum"); } - public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseQRankSum", 1, VCFHeaderLineType.Float, "Phred-scaled p-value From Wilcoxon Rank Sum Test of Alt Vs. Ref base qualities")); } + public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseQRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities")); } protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List refQuals, List altQuals) { for ( final PileupElement p : pileup ) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java index 2d130e939..7563a89b1 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java @@ -13,7 +13,7 @@ public class MappingQualityRankSumTest extends RankSumTest { public List getKeyNames() { return Arrays.asList("MQRankSum"); } - public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("MQRankSum", 1, VCFHeaderLineType.Float, "Phred-scaled p-value From Wilcoxon Rank Sum Test of Alt Vs. Ref read mapping qualities")); } + public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("MQRankSum", 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities")); } protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List refQuals, List altQuals) { for ( final PileupElement p : pileup ) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java index eefe70214..b1a86ecf0 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java @@ -18,8 +18,6 @@ import java.util.HashMap; public abstract class RankSumTest implements InfoFieldAnnotation, StandardAnnotation { - private static final double minPValue = 1e-20; - public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; @@ -52,15 +50,9 @@ public abstract class RankSumTest implements InfoFieldAnnotation, StandardAnnota // we are testing that set1 (the alt bases) have lower quality scores than set2 (the ref bases) final Pair testResults = mannWhitneyU.runOneSidedTest( MannWhitneyU.USet.SET1 ); - double pvalue = testResults.second; - - // deal with precision issues - if ( pvalue < minPValue ) { - pvalue = minPValue; - } final Map map = new HashMap(); - map.put(getKeyNames().get(0), String.format("%.3f", Math.abs(QualityUtils.phredScaleErrorRate(pvalue)))); + map.put(getKeyNames().get(0), String.format("%.3f", testResults.first)); return map; } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java index e67061e48..683223044 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java @@ -19,7 +19,7 @@ public class ReadPosRankSumTest extends RankSumTest { public List getKeyNames() { return Arrays.asList("ReadPosRankSum"); } - public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ReadPosRankSum", 1, VCFHeaderLineType.Float, "Phred-scaled p-value From Wilcoxon Rank Sum Test of Alt Vs. Ref read position bias")); } + public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ReadPosRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias")); } protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List refQuals, List altQuals) { for ( final PileupElement p : pileup ) { 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 18fb728ca..9ecd3cdbe 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("7e6dc39a191851f41d23753c4cca37a3")); + Arrays.asList("11fab4bbd26e0428e6d7b53284a34388")); 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("21f01de76f113627c1fa60d7954df871")); + Arrays.asList("4fb98442f2c09247fab296872abb5655")); 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("e5fccc9d2c8f21ab494aa2f878a5f197")); + Arrays.asList("4bcc71f014def02d0fe9237176cc99af")); 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("76348339e6dd750308647d8c126c6f4c")); + Arrays.asList("c92e614ec796a5b39c5fdcc426410a9b")); 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("e82ea45f1eef16b6ebf7def2171ee613")); + Arrays.asList("6c0d9d61f09d6b9036cdadf3f86f5e66")); executeTest("test overwriting header", spec); } @@ -87,7 +87,7 @@ 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("426c0f2f8b94bdb50736519769a11355")); + Arrays.asList("019d6b1bb7b367759fc42fbdb14b8bf7")); executeTest("not passing it any reads", spec); } @@ -95,7 +95,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTagWithDbsnp() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, - Arrays.asList("f11c43c69e6aca81d7ec98d7ac39e5f6")); + Arrays.asList("92a29447f222eadb549dc05ddd11b45e")); executeTest("getting DB tag with dbSNP", spec); } @@ -103,7 +103,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTagWithHapMap() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, - Arrays.asList("921ff533873c37acd3849f56e41ebeec")); + Arrays.asList("067dde55de98a631225e0e084f0fcc1a")); executeTest("getting DB tag with HM3", spec); } @@ -111,7 +111,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testUsingExpression() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1, - Arrays.asList("8ea6f267094ab334ec0415a9177e2588")); + Arrays.asList("e55b457426d6ba7f8ccea085c23c1350")); executeTest("using expression", 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 d1f587a20..7b4244896 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -27,13 +27,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { 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("02481347a19d80e09538f2f6aa1be74a")); + Arrays.asList("a1add49e71306d72252ee3af3c40d2da")); executeTest("test MultiSample Pilot1", spec); } @Test public void testMultiSamplePilot2AndRecallingWithAlleles() { - String md5 = "d50bc17991d0dfd03ab2810a1cfeec85"; + String md5 = "87a99063152ca935a1bec87ef19e0dad"; WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1, @@ -52,12 +52,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testWithAllelesPassedIn() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("bcb02e2a969edfbd290b9ec22f1a5884")); + Arrays.asList("a2584e8f92efa056cd8a09814476f883")); executeTest("test MultiSample Pilot2 with alleles passed in", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("f1ff29ac1c79c76fcb6c290b39bc3a18")); + Arrays.asList("0d15caf026c74bf859900e717b7fe996")); executeTest("test MultiSample Pilot2 with alleles passed in", spec2); } @@ -65,7 +65,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testSingleSamplePilot2() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -glm SNP -L 1:10,000,000-10,100,000", 1, - Arrays.asList("a7f59c32f63e8ca4c3ffe468c51fbaa2")); + Arrays.asList("2241d97972b72233cb7b4c565739698e")); executeTest("test SingleSample Pilot2", spec); } @@ -75,7 +75,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - private final static String COMPRESSED_OUTPUT_MD5 = "211e4ed67cd7bd3501555d829548da48"; + private final static String COMPRESSED_OUTPUT_MD5 = "64fd80527aa1b00fbbb4a77f1d5df48c"; @Test public void testCompressedOutput() { @@ -136,9 +136,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testCallingParameters() { HashMap e = new HashMap(); - e.put( "--min_base_quality_score 26", "e74b0f3c3977f383645e82ae76034932" ); - e.put( "--min_mapping_quality_score 26", "5f08d9e052bdb04a2a5ee78db349dde9" ); - e.put( "--p_nonref_model GRID_SEARCH", "2f1350f76a571d28cd06e59ea6dffe4b" ); + e.put( "--min_base_quality_score 26", "f91280e3c12646207b3d06f9a563699b" ); + e.put( "--min_mapping_quality_score 26", "6f9e99469ec5f5ef333a5075e8149674" ); + e.put( "--p_nonref_model GRID_SEARCH", "430cfe737affe6b179725e1eb0b95655" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -151,9 +151,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOutputParameter() { HashMap e = new HashMap(); - e.put( "-sites_only", "63b76c4d26edf8cbb5bd91dafc81fee1" ); - e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "5bf0268945d953377ea3a811b20ff1bc" ); - e.put( "--output_mode EMIT_ALL_SITES", "78eeff5b2277877954e4985934077d3f" ); + e.put( "-sites_only", "81e01f685e98d8f18fa288beb1246881" ); + e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "3916157145aea448a38e4f12a0c381ae" ); + e.put( "--output_mode EMIT_ALL_SITES", "7652e2362e7fc038bc0f41a03df5d9f4" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -167,12 +167,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { 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("5f08d9e052bdb04a2a5ee78db349dde9")); + Arrays.asList("6f9e99469ec5f5ef333a5075e8149674")); executeTest("test confidence 1", 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("0d0bbfd08d1ce35ec1c007ba0f8dfe37")); + Arrays.asList("c2020de023bb3d731e17ed97aaa85c3d")); executeTest("test confidence 2", spec2); } @@ -184,8 +184,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testHeterozyosity() { HashMap e = new HashMap(); - e.put( 0.01, "4fb6e66895bbaa9a3b9af91c985a2782" ); - e.put( 1.0 / 1850, "1397d29d924e74f43de466927a9f7915" ); + e.put( 0.01, "a56d3790bb2e18cec5a3099079431f19" ); + e.put( 1.0 / 1850, "119dff78b9f3b415ef3ed9d1bc46dd04" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -209,7 +209,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("b44ddfbeb9fc413e44194799b3e3bbf8")); + Arrays.asList("cd84c86ed02e4b052b96f76270ffd7fc")); executeTest(String.format("test multiple technologies"), spec); } @@ -228,7 +228,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq CALCULATE_AS_NECESSARY", 1, - Arrays.asList("164e25d61ef562ae863871d4ec7cb387")); + Arrays.asList("9b71db6bebce80022c8fde5db09de65f")); executeTest(String.format("test calling with BAQ"), spec); } @@ -248,7 +248,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -glm INDEL" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("08b63c534a7e129e53cdd1527d51be5c")); + Arrays.asList("84bc209f38d60f325f1a8b6292a82c82")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -263,7 +263,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -glm INDEL -minIndelCnt 1" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("b6546f6e8f092b3c39cffec22aa47bcb")); + Arrays.asList("f536ca23cb86b14fc20e453859dafc01")); executeTest(String.format("test indel caller in SLX witn low min allele count"), spec); } @@ -277,7 +277,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -glm INDEL" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("1d1ddad622dbee7e74550b5bb9d0928f")); + Arrays.asList("e9b4fef2cdfa4c4657f0df53309131b6")); executeTest(String.format("test indel calling, multiple technologies"), spec); }