diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java index 8098de5b1..ab38b69cd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java @@ -49,5 +49,5 @@ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnno public List getKeyNames() { return Arrays.asList(VCFConstants.DEPTH_KEY); } - public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Filtered Depth")); } + public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Approximate read depth; some reads may have been filtered")); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index bdd4e2c65..369c2d0c6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -258,7 +258,7 @@ public class UnifiedGenotyper extends LocusWalker result = new HashSet(); result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype")); result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality")); - result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)")); + result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Approximate read depth (reads with MQ=255 or with bad mates are filtered)")); result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification")); return result; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 919e3d9bd..3bfb81dd0 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("8e7de435105499cd71ffc099e268a83e")); + Arrays.asList("9beb795536e95954f810835c6058f2ad")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -40,7 +40,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant:VCF3 " + 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("64b6804cb1e27826e3a47089349be581")); + Arrays.asList("2977bb30c8b84a5f4094fe6090658561")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -64,7 +64,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("fd1ffb669800c2e07df1e2719aa38e49")); + Arrays.asList("49d989f467b8d6d8f98f7c1b67cd4a05")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @@ -72,7 +72,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant:VCF3 " + 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("09f8e840770a9411ff77508e0ed0837f")); + Arrays.asList("0948cd1dba7d61f283cc4cf2a7757d92")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } @@ -80,7 +80,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testExcludeAnnotations() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("b49fe03aa4b675db80a9db38a3552c95")); + Arrays.asList("33062eccd6eb73bc49440365430454c4")); executeTest("test exclude annotations", spec); } @@ -88,7 +88,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testOverwritingHeader() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1, - Arrays.asList("78d2c19f8107d865970dbaf3e12edd92")); + Arrays.asList("062155edec46a8c52243475fbf3a2943")); executeTest("test overwriting header", spec); } @@ -96,7 +96,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoReads() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1, - Arrays.asList("16e3a1403fc376320d7c69492cad9345")); + Arrays.asList("06635f2dd91b539bfbce9bf7914d8e43")); executeTest("not passing it any reads", spec); } @@ -104,7 +104,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTagWithDbsnp() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1, - Arrays.asList("3da8ca2b6bdaf6e92d94a8c77a71313d")); + Arrays.asList("820eeba1f6e3a0758a69d937c524a38e")); executeTest("getting DB tag with dbSNP", spec); } @@ -112,7 +112,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTagWithHapMap() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --comp:H3 " + validationDataLocation + "fakeHM3.vcf -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1, - Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688")); + Arrays.asList("31cc2ce157dd20771418c08d6b3be1fa")); executeTest("getting DB tag with HM3", spec); } @@ -120,7 +120,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testUsingExpression() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -L " + validationDataLocation + "vcfexample3empty.vcf", 1, - Arrays.asList("ae30a1ac7bfbc3d22a327f8b689cad31")); + Arrays.asList("074865f8f8c0ca7bfd58681f396c49e9")); executeTest("using expression", spec); } @@ -128,7 +128,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testUsingExpressionWithID() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.ID -L " + validationDataLocation + "vcfexample3empty.vcf", 1, - Arrays.asList("1b4921085b26cbfe07d53b7c947de1e5")); + Arrays.asList("97b26db8135d083566fb585a677fbe8a")); executeTest("using expression with ID", spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index b80f214b1..0197f94e5 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -5,10 +5,8 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.annotations.Test; -import java.io.File; import java.util.Arrays; import java.util.HashMap; -import java.util.List; import java.util.Map; // ********************************************************************************** // @@ -30,7 +28,7 @@ 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("b27939251539439a382538e507e03507")); + Arrays.asList("364a6112e6034571a896d4c68b6ff02a")); executeTest("test MultiSample Pilot1", spec); } @@ -38,12 +36,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testWithAllelesPassedIn() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("8de2602679ffc92388da0b6cb4325ef6")); + Arrays.asList("6cce55734ecd1a56c33f0ecba67d1258")); 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 -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("6458f3b8fe4954e2ffc2af972aaab19e")); + Arrays.asList("b2a00130a4b6f9a3c31288a236f5d159")); executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2); } @@ -51,7 +49,7 @@ 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 -L 1:10,000,000-10,100,000", 1, - Arrays.asList("6762b72ae60155ad71738d7c76b80e4b")); + Arrays.asList("3ccce5d909f8f128e496f6841836e5f7")); executeTest("test SingleSample Pilot2", spec); } @@ -61,7 +59,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - private final static String COMPRESSED_OUTPUT_MD5 = "bc71dba7bbdb23e7d5cc60461fdd897b"; + private final static String COMPRESSED_OUTPUT_MD5 = "890143b366050e78d6c6ba6b2c6b6864"; @Test public void testCompressedOutput() { @@ -82,7 +80,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // Note that we need to turn off any randomization for this to work, so no downsampling and no annotations - String md5 = "b9504e446b9313559c3ed97add7e8dc1"; + String md5 = "95614280c565ad90f8c000376fef822c"; WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1, @@ -113,8 +111,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testCallingParameters() { HashMap e = new HashMap(); - e.put( "--min_base_quality_score 26", "bb3f294eab3e2cf52c70e63b23aac5ee" ); - e.put( "--computeSLOD", "eb34979efaadba1e34bd82bcacf5c722" ); + e.put( "--min_base_quality_score 26", "7acb1a5aee5fdadb0cc0ea07a212efc6" ); + e.put( "--computeSLOD", "e9d23a08472e4e27b4f25e844f5bad57" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -127,9 +125,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOutputParameter() { HashMap e = new HashMap(); - e.put( "-sites_only", "d40114aa201aa33ff5f174f15b6b73af" ); - e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "3c681b053fd2280f3c42041d24243752" ); - e.put( "--output_mode EMIT_ALL_SITES", "eafa6d71c5ecd64dfee5d7a3f60e392e" ); + e.put( "-sites_only", "44f3b5b40e6ad44486cddfdb7e0bfcd8" ); + e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "94e53320f14c5ff29d62f68d36b46fcd" ); + e.put( "--output_mode EMIT_ALL_SITES", "73ad1cc41786b12c5f0e6f3e9ec2b728" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -143,12 +141,12 @@ 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("c71ca370947739cb7d87b59452be7a07")); + Arrays.asList("902327e8a45fe585c8dfd1a7c4fcf60f")); 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("1c0a599d475cc7d5e745df6e9b6c0d29")); + Arrays.asList("9ef66764a0ecfe89c3e4e1a93a69e349")); executeTest("test confidence 2", spec2); } @@ -160,8 +158,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testHeterozyosity() { HashMap e = new HashMap(); - e.put( 0.01, "f84da90c310367bd51f2ab6e346fa3d8" ); - e.put( 1.0 / 1850, "5791e7fef40d4412b6d8f84e0a809c6c" ); + e.put( 0.01, "46243ecc2b9dc716f48ea280c9bb7e72" ); + e.put( 1.0 / 1850, "6b2a59dbc76984db6d4d6d6b5ee5d62c" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -185,7 +183,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("9cc9538ac83770e12bd0830d285bfbd0")); + Arrays.asList("f0fbe472f155baf594b1eeb58166edef")); executeTest(String.format("test multiple technologies"), spec); } @@ -204,7 +202,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq CALCULATE_AS_NECESSARY", 1, - Arrays.asList("eaf8043edb46dfbe9f97ae03baa797ed")); + Arrays.asList("8c87c749a7bb5a76ed8504d4ec254272")); executeTest(String.format("test calling with BAQ"), spec); } @@ -223,7 +221,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("eeba568272f9b42d5450da75c7cc6d2d")); + Arrays.asList("a64d2e65b5927260e4ce0d948760cc5c")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -238,7 +236,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -minIndelCnt 1" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("5fe98ee853586dc9db58f0bc97daea63")); + Arrays.asList("2ad52c2e75b3ffbfd8f03237c444e8e6")); executeTest(String.format("test indel caller in SLX with low min allele count"), spec); } @@ -251,7 +249,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("19ff9bd3139480bdf79dcbf117cf2b24")); + Arrays.asList("69107157632714150fc068d412e31939")); executeTest(String.format("test indel calling, multiple technologies"), spec); } @@ -261,7 +259,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("118918f2e9e56a3cfc5ccb2856d529c8")); + Arrays.asList("84f065e115004e4c9d9d62f1bf6b4f44")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1); } @@ -271,7 +269,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("a20799237accd52c1b8c2ac096309c8f")); + Arrays.asList("7ea8372e4074f90ec942f964e1863351")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2); } @@ -281,7 +279,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1, - Arrays.asList("18ef8181157b4ac3eb8492f538467f92")); + Arrays.asList("94afa8c011b47af7323c821bf19106b4")); executeTest("test MultiSample Pilot2 indels with complicated records", spec3); } @@ -290,7 +288,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec( baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation + "phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1, - Arrays.asList("ad884e511a751b05e64db5314314365a")); + Arrays.asList("1e02f57fafaa41db71c531eb25e148e1")); executeTest("test MultiSample 1000G Phase1 indels with complicated records emitting all sites", spec4); }