diff --git a/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java b/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java index f9dbc36c4..ecb381e3f 100755 --- a/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java +++ b/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java @@ -298,7 +298,7 @@ public class MannWhitneyU { public static Pair calculatePRecursively(int n, int m, long u, boolean twoSided, ExactMode mode) { if ( m > 8 && n > 5 ) { throw new StingException(String.format("Please use the appropriate (normal or sum of uniform) approximation. Values n: %d, m: %d",n,m)); } double p = mode == ExactMode.POINT ? cpr(n,m,u) : cumulativeCPR(n,m,u); - p *= twoSided ? 2.0 : 1.0; + //p *= twoSided ? 2.0 : 1.0; double z; try { 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 fc97a285a..8e5ff09e3 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G \"Standard\" -B: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("f559fa1754f82a00454894ecd518a3b0")); + Arrays.asList("248233148af03e39f104bfb161899136")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -71,7 +71,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G \"Standard\" -B: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("709a1f482cce68992c637da3cff824a8")); + Arrays.asList("25068fff13c928ca1b70e5d67af32775")); executeTest("test file doesn't have annotations, asking for annotations, #2", 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 fa2e9c687..06d76f4c3 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -34,7 +34,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testMultiSamplePilot2AndRecallingWithAlleles() { - String md5 = "24876505e3526a58fc709ecf44372cfb"; + String md5 = "00bf111cb80f1acb29679647f9433e2f"; 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, @@ -66,7 +66,7 @@ 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("3474828a82c070242346b78dc8b760c9")); + Arrays.asList("61db698ea6d11deba2fc900bd544b082")); executeTest("test SingleSample Pilot2", spec); } @@ -76,7 +76,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - private final static String COMPRESSED_OUTPUT_MD5 = "a5e0673fdda01a1bcdfe122299c734f9"; + private final static String COMPRESSED_OUTPUT_MD5 = "af5e98318f56e203b25361fee4d41548"; @Test public void testCompressedOutput() { @@ -138,8 +138,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testCallingParameters() { HashMap e = new HashMap(); e.put( "--min_base_quality_score 26", "93ad1ed265be26e0c1fe05975d01edd1" ); - e.put( "--min_mapping_quality_score 26", "01882d04939a5a6085fc5cadec019d3e" ); - e.put( "--p_nonref_model GRID_SEARCH", "7b0b7f536c66afe006174ff9a094dd95" ); + e.put( "--min_mapping_quality_score 26", "8f470d3622c0eb9fcc78b9ef3c9b0a0d" ); + e.put( "--p_nonref_model GRID_SEARCH", "cb8f353e0b1c252ef09dcbebe50d95af" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -152,9 +152,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOutputParameter() { HashMap e = new HashMap(); - e.put( "-sites_only", "919d4b034ef0e07c8d50ea05b8fa0725" ); - e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "b793fca3450c0afcde2418d79bbf2724" ); - e.put( "--output_mode EMIT_ALL_SITES", "6e47e30c029e4bba63a492d7deb022f2" ); + e.put( "-sites_only", "71f61655f725cda56bc46d99d1cc24eb" ); + e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "8193a4c06ddbd82d0a328491118b16a8" ); + e.put( "--output_mode EMIT_ALL_SITES", "89859bd987e8b797d37f5dec54d37e9c" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -168,12 +168,12 @@ 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("01882d04939a5a6085fc5cadec019d3e")); + Arrays.asList("8f470d3622c0eb9fcc78b9ef3c9b0a0d")); 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("00807e8a5bc9172c34a5b4bd2e8afba7")); + Arrays.asList("50d03e71ed2b4eb20db82e22541ac2f2")); executeTest("test confidence 2", spec2); } @@ -185,8 +185,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testHeterozyosity() { HashMap e = new HashMap(); - e.put( 0.01, "966ceb5a7a6d87ad417046c2f60e69fd" ); - e.put( 1.0 / 1850, "85057e3f2df0433392409c586af1be33" ); + e.put( 0.01, "649590cbfc67bddf82416a0b82027696" ); + e.put( 1.0 / 1850, "22153b7d06d13ea1a1ffdc45d7668974" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -210,7 +210,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("f9d92a81294569b9c918848932c1a0ca")); + Arrays.asList("d453f2e44fb7f0ec027c2a5f791da6aa")); executeTest(String.format("test multiple technologies"), spec); } @@ -229,7 +229,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq CALCULATE_AS_NECESSARY", 1, - Arrays.asList("930dc1d9bc2006b86e8c90a50d349151")); + Arrays.asList("60cc4c793caaf891075d862a2376d73c")); executeTest(String.format("test calling with BAQ"), spec); } @@ -243,7 +243,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq OFF", 1, - Arrays.asList("f9d92a81294569b9c918848932c1a0ca")); + Arrays.asList("d453f2e44fb7f0ec027c2a5f791da6aa")); executeTest(String.format("test calling with BAQ OFF"), spec); }