From 2c3c680eb704348cb8e20572f5b9d2fb3a5a986c Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 5 Jun 2013 12:22:14 -0400 Subject: [PATCH] Misc changes and cleanup from all previous commits in this push. 1. By default, do not include the UG CEU callset for assessment. 2. Updated md5s that are different now with all the HC changes. --- ...lexAndSymbolicVariantsIntegrationTest.java | 6 +++--- .../HaplotypeCallerIntegrationTest.java | 20 +++++++++---------- ...aplotypeCallerParallelIntegrationTest.java | 2 +- 3 files changed, 14 insertions(+), 14 deletions(-) diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java index fba294c3d..073d54ec5 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java @@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleComplex1() { - HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "8d7728909b1b8eb3f30f2f1583f054a8"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "d21f15a5809fe5259af41ae6774af6f1"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { @@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleGGAComplex() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538", - "db71826dc798ff1cdf0c5d05b0ede976"); + "d4a0797c2fd4c103bf9a137633376156"); } @Test public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", - "42831d5463552911b7da9de0b4a27289"); + "a9872228d0275a30f5a1f7e070a9c9f4"); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index 904f15728..dbdd0afcd 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -78,12 +78,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "1b15e4647013ab2c3ce7073c420d8640"); + HCTest(CEUTRIO_BAM, "", "e9167a1bfc0fc276586788d1ce1be408"); } @Test public void testHaplotypeCallerSingleSample() { - HCTest(NA12878_BAM, "", "423be27dc2cf7fd10baf465cf93e18e2"); + HCTest(NA12878_BAM, "", "b1d46afb9659ac3b92a3d131b58924ef"); } @Test(enabled = false) // can't annotate the rsID's yet @@ -94,7 +94,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSampleGGA() { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", - "a28e6f14e28708283d61c1e423bbdcb1"); + "d83856b8136776bd731a8037c16b71fa"); } @Test @@ -110,7 +110,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleIndelQualityScores() { - HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "8344d86751b707c53b296c297eba4bfa"); + HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "70c4476816f5d35c9978c378dbeac09b"); } private void HCTestNearbySmallIntervals(String bam, String args, String md5) { @@ -147,7 +147,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerNearbySmallIntervals() { - HCTestNearbySmallIntervals(NA12878_BAM, "", "dea98f257d39fa1447a12c36a6bbf4a3"); + HCTestNearbySmallIntervals(NA12878_BAM, "", "947aae309ecab7cd3f17ff9810884924"); } // This problem bam came from a user on the forum and it spotted a problem where the ReadClipper @@ -157,14 +157,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void HCTestProblematicReadsModifiedInActiveRegions() { final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965"; - final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("7cd1c5e2642ae8ddf38932aba1f51d69")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("0689d2c202849fd05617648eaf429b9a")); executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec); } @Test public void HCTestStructuralIndels() { final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730"; - final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ee55ff4c6ec1bbef88e21cc0f45d4c47")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("91717e5e271742c2c9b67223e58f1320")); executeTest("HCTestStructuralIndels: ", spec); } @@ -186,7 +186,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestReducedBam() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1, - Arrays.asList("4886a98bf699f4e7f4491160749ada6a")); + Arrays.asList("0124c4923d96ec0f8222b596dd4ef534")); executeTest("HC calling on a ReducedRead BAM", spec); } @@ -194,7 +194,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void testReducedBamWithReadsNotFullySpanningDeletion() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1, - Arrays.asList("86bdd07a3ac4f6ce239c30efea8bf5ba")); + Arrays.asList("0e020dcfdf249225714f5cd86ed3869f")); executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec); } @@ -208,7 +208,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestDBSNPAnnotationWGS() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1, - Arrays.asList("7b23a288a31cafca3946f14f2381e7cb")); + Arrays.asList("446a786bb539f3ec2084dd75167568aa")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java index ff5a501cc..62e685eab 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java @@ -61,7 +61,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest { List tests = new ArrayList(); for ( final int nct : Arrays.asList(1, 2, 4) ) { - tests.add(new Object[]{nct, "c277fd65365d59b734260dd8423313bb"}); + tests.add(new Object[]{nct, "ef42a438b82681d1c0f921c57e16ff12"}); } return tests.toArray(new Object[][]{});