From b51762c27908c9734c47bc775dbed44109a87d6f Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 12 Nov 2010 14:41:10 +0000 Subject: [PATCH] When you commit code late at night you tend to make careless mistakes... like forgetting to update integration tests. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4658 348d0f76-0448-11de-a6fe-93d51630548a --- .../VariantAnnotatorIntegrationTest.java | 4 ++-- .../walkers/beagle/BeagleIntegrationTest.java | 4 ++-- .../CombineVariantsIntegrationTest.java | 16 ++++++++-------- 3 files changed, 12 insertions(+), 12 deletions(-) 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 146c1c817..877bf9d6f 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("bcd5c80e54d90f1ddf65e0c47b0710a5")); + Arrays.asList("a7680de85e0b118415bcd032b3b49688")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -63,7 +63,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("10ceed55fd51f104d4b57aa555770253")); + Arrays.asList("207a5af3647f1f0769fdd4dd6bd0c132")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java index 71c1ba393..a4e2b6c91 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java @@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest { "-B:beagleR2,BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " + "-B:beagleProbs,BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " + "-B:beaglePhased,BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " + - "-o %s -NO_HEADER", 1, Arrays.asList("e04d9768cdb94d1f0e2e35a7f1bc49ab")); + "-o %s -NO_HEADER", 1, Arrays.asList("93546f4f6a7f5fe24f01a357dcad7c5f")); executeTest("test BeagleOutputToVCF", spec); } @@ -72,7 +72,7 @@ public class BeagleIntegrationTest extends WalkerTest { "-B:beagleR2,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+ "-B:beagleProbs,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+ "-B:beaglePhased,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+ - "-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("fd104b7da9e6c99b662c6ad746fd53f3")); + "-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("f8071eda9f762947c6a3404d6d126df2")); executeTest("testBeagleChangesSitesToRef",spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index e43914eb1..0f0864a62 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -60,21 +60,21 @@ public class CombineVariantsIntegrationTest extends WalkerTest { } - @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "def6365e318cb506aa69ee8ec6899c4e"); } - @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "6d1d9fffcc10d4f9ab086760603b577e", " -setKey foo"); } - @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "e1d43e0c4df65df5e9761916b12f0b5b", " -setKey null"); } + @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "3287ddd7c5003b3c791048cb2532578a"); } + @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1b8b58c2b231926f0ba45d29c5242df5", " -setKey foo"); } + @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "5aaa695bc1754d6abcbed27f0c0b4c64", " -setKey null"); } @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "79e7e474b0a2bb82930201f143328d5d"); } // official project VCF files in tabix format @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "d93ee8b9f36eedc80a3afa548bffc888"); } - @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "4d16ffe9cf3beff94ac05ea49f85049a"); } + @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "26c99206407fb2c42beadcac5e5de246"); } - @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "78f2a2c09df8fa51ccfe5b3706a5e313"); } // official project VCF files in tabix format + @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "9b44bb39702b41240371815320e452d5"); } // official project VCF files in tabix format @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "460bdbeaf7e9641395ac2ce6e1afc106"); } // official project VCF files in tabix format - @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "d445583e7f3a8bc98004e8e44878fce6"); } + @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "02f0634d0176138e4195009eff7f2308"); } - @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e64284f598fc4f473ee5554282d84b0c"); } + @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "d443358367211b96762ae64d1461b587"); } - @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "1f3d118dcee9b711714856639930694d"); } + @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "ff7bdac468045715d4ac0309d8736c23"); } @Test public void threeWayWithRefs() { WalkerTestSpec spec = new WalkerTestSpec(