From fde7d36926b1ace076d54a01086714c25ab704ed Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 26 Mar 2013 22:07:25 -0400 Subject: [PATCH] Updating md5s due to changes in assembly graph creation algorithms and default parameter --- ...omplexAndSymbolicVariantsIntegrationTest.java | 8 ++++---- .../HaplotypeCallerIntegrationTest.java | 16 ++++++++-------- 2 files changed, 12 insertions(+), 12 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 830152903..3aaffdeaa 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 @@ -63,7 +63,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleComplex() { - HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "6dd29d6fec056419ab0fa03a7d43d85e"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "f9fa4d3c88fd9c0f23c7a3ddd3d24a8c"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { @@ -75,7 +75,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa // TODO -- need a better symbolic allele test @Test public void testHaplotypeCallerSingleSampleSymbolic() { - HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "8225fb59b9fcbe767a473c9eb8b21537"); + HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "e746a38765298acd716194aee4d93554"); } private void HCTestComplexGGA(String bam, String args, String md5) { @@ -87,12 +87,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleGGAComplex() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538", - "84616464aed68f4d9bc9e08472eff9c0"); + "e8ffbfae3c1af5be02631a31f386a431"); } @Test public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", - "e2d1023b846bfac31b4f7a3a4b90d931"); + "c3a98b19efa7cb36fe5f5f2ab893ef56"); } } 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 1b98b2239..c5614d405 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 @@ -69,12 +69,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "9859b136d05085b5ec0833035289106a"); + HCTest(CEUTRIO_BAM, "", "45856ad67bfe8d8bea45808d8258bcf1"); } @Test public void testHaplotypeCallerSingleSample() { - HCTest(NA12878_BAM, "", "27f660bf1c9a6ed7167d77022d401b73"); + HCTest(NA12878_BAM, "", "b6c93325f851ac358ea49260fb11b75c"); } @Test(enabled = false) // can't annotate the rsID's yet @@ -85,7 +85,7 @@ 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", - "e25fc2196401a16347e0c730dbcbe828"); + "4ca6b560d0569cdca400d3e50915e211"); } private void HCTestIndelQualityScores(String bam, String args, String md5) { @@ -96,7 +96,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleIndelQualityScores() { - HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "325d7d73e0bd86b6cb146b249eda959a"); + HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "5d06ec5502d3f157964bd7b275d6a0cb"); } @Test @@ -111,14 +111,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void HCTestProblematicReadsModifiedInActiveRegions() { final String base = String.format("-T HaplotypeCaller -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("0689d2c202849fd05617648eaf429b9a")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("53a50dae68f0175ca3088dea1d3bb881")); executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec); } @Test public void HCTestStructuralIndels() { final String base = String.format("-T HaplotypeCaller -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("ec97a0a65890169358842e765ff8dd15")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("d3bc6adde8cd9514ae5c49cd366d5de4")); executeTest("HCTestStructuralIndels: ", spec); } @@ -140,7 +140,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestReducedBam() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller -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("5280f1a50ca27d8e435da0bd5b26ae93")); + Arrays.asList("4adb833ed8af20224b76bba61e2b0d93")); executeTest("HC calling on a ReducedRead BAM", spec); } @@ -148,7 +148,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void testReducedBamWithReadsNotFullySpanningDeletion() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1, - Arrays.asList("addceb63f5bfa9f11e15335d5bf641e9")); + Arrays.asList("1704b0901c86f8f597d931222d5c8dd8")); executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec); } }