From caf15fb7276485f11336e292e1a44dc912c0c70f Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 5 Apr 2013 14:11:06 -0400 Subject: [PATCH] Update MD5s to reflect new HC algorithms and parameter values --- ...lexAndSymbolicVariantsIntegrationTest.java | 6 +++--- .../HaplotypeCallerIntegrationTest.java | 21 +++++++++++-------- 2 files changed, 15 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 a891220c5..ff2b3d0b6 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 testHaplotypeCallerMultiSampleComplex() { - HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "7b67ac6213b7a6f759057fb9d7148fdc"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "80b9280b1e65952f60ba2fd738d4840f"); } 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", - "eb41ed6f1d692368a0f67311d139a38a"); + "125e93deeb3b390a14d9b777aa2a220f"); } @Test public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", - "c4c33c962aca12c51def9b8cde35b7d2"); + "6957fd0e8a5bc66d2572a6ca8626fa7a"); } } 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 51c3296ac..5fc8c5622 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 @@ -47,12 +47,15 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; import net.sf.picard.reference.IndexedFastaSequenceFile; +import org.broad.tribble.TribbleIndexedFeatureReader; import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFCodec; import org.testng.annotations.Test; import java.io.File; @@ -77,12 +80,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "f132843e3c8e065a783cc4fdf9ee5df3"); + HCTest(CEUTRIO_BAM, "", "6fa37c449a800bcd59069be03ad2fff2"); } @Test public void testHaplotypeCallerSingleSample() { - HCTest(NA12878_BAM, "", "15e0201f5c478310d278d2d03483c152"); + HCTest(NA12878_BAM, "", "6140447b34bd1d08b3ed4d473d2c2f23"); } @Test(enabled = false) // can't annotate the rsID's yet @@ -93,7 +96,7 @@ 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", - "48d309aed0cdc40cc983eeb5a8d12f53"); + "cbd119f3d37a9af0b3539c13b8053bd9"); } @Test @@ -109,7 +112,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleIndelQualityScores() { - HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "34c7fcfe17a1d835e2dc403df9eb3591"); + HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "9eeeada2f7145adfe08f538aad704982"); } private void HCTestNearbySmallIntervals(String bam, String args, String md5) { @@ -146,7 +149,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerNearbySmallIntervals() { - HCTestNearbySmallIntervals(NA12878_BAM, "", "eae65d20836d6c6ebca9e25e33566f74"); + HCTestNearbySmallIntervals(NA12878_BAM, "", "16ecd2f282bcb10dc32e7f3fe714a000"); } // This problem bam came from a user on the forum and it spotted a problem where the ReadClipper @@ -156,14 +159,14 @@ 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("a3d74040a4966bf7a04cbd4924970685")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("0689d2c202849fd05617648eaf429b9a")); 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("40da88ed3722c512264b72db37f18720")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("e8466846ca420bcbcd52b97f7a661aa3")); executeTest("HCTestStructuralIndels: ", spec); } @@ -185,7 +188,7 @@ 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("69b83d578c14ed32d08ce4e7ff8a8a18")); + Arrays.asList("e30b974b038293841e6be23c93ce76e1")); executeTest("HC calling on a ReducedRead BAM", spec); } @@ -193,7 +196,7 @@ 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("0cae60d86a3f86854699217a30ece3e3")); + Arrays.asList("a913849c7ebdefb23ef9fa5ec05960fd")); executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec); } }