From 6cfb2d1393625d9d3a5d7c6fb4bf6eee2be839d3 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 6 Jun 2012 14:10:35 -0400 Subject: [PATCH] Restoring SelectVariantsIntegrationTest --- .../SelectVariantsIntegrationTest.java | 355 +++++++++--------- 1 file changed, 178 insertions(+), 177 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index 8203b089b..92a9f3739 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -10,128 +10,129 @@ public class SelectVariantsIntegrationTest extends WalkerTest { return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s --no_cmdline_in_header" + args; } -// @Test -// public void testComplexSelection() { -// String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; -// String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; -// -// WalkerTestSpec spec = new WalkerTestSpec( -// baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile), -// 1, -// Arrays.asList("6cd82274335eeb0b449e571f38d54d3a") -// ); -// spec.disableShadowBCF(); -// executeTest("testComplexSelection--" + testfile, spec); -// } -// -// @Test -// public void testSampleExclusion() { -// String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; -// String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; -// -// WalkerTestSpec spec = new WalkerTestSpec( -// "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sn A -xl_sf " + samplesFile + " --variant " + testfile, -// 1, -// Arrays.asList("bbd7b28d1c5701e17b395d64f8b6f13d") -// ); -// spec.disableShadowBCF(); -// -// executeTest("testSampleExclusion--" + testfile, spec); -// } -// -// @Test -// public void testRepeatedLineSelection() { -// String testfile = testDir + "test.dup.vcf"; -// -// WalkerTestSpec spec = new WalkerTestSpec( -// baseTestString(" -sn A -sn B -sn C --variant " + testfile), -// 1, -// Arrays.asList("77579c53dbde4e8171f3cee83b98351b") -// ); -// -// executeTest("testRepeatedLineSelection--" + testfile, spec); -// } -// -// @Test -// public void testDiscordance() { -// String testFile = testDir + "NA12878.hg19.example1.vcf"; -// -// WalkerTestSpec spec = new WalkerTestSpec( -// "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header", -// 1, -// Arrays.asList("03abdc27bfd7aa36d57bba0325b31e0d") -// ); -// spec.disableShadowBCF(); -// -// executeTest("testDiscordance--" + testFile, spec); -// } -// -// @Test -// public void testDiscordanceNoSampleSpecified() { -// String testFile = testDir + "NA12878.hg19.example1.vcf"; -// -// WalkerTestSpec spec = new WalkerTestSpec( -// "-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header", -// 1, -// Arrays.asList("9fb54ed003234a5847c565ffb6767b95") -// ); -// spec.disableShadowBCF(); -// -// executeTest("testDiscordanceNoSampleSpecified--" + testFile, spec); -// } -// -// @Test -// public void testConcordance() { -// String testFile = testDir + "NA12878.hg19.example1.vcf"; -// -// WalkerTestSpec spec = new WalkerTestSpec( -// "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc " + b37hapmapGenotypes + " --variant " + testFile + " -o %s --no_cmdline_in_header", -// 1, -// Arrays.asList("76857b016198c3e08a2e27bbdb49f3f0") -// ); -// spec.disableShadowBCF(); -// -// executeTest("testConcordance--" + testFile, spec); -// } -// -// @Test -// public void testVariantTypeSelection() { -// String testFile = testDir + "complexExample1.vcf"; -// -// WalkerTestSpec spec = new WalkerTestSpec( -// "-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s --no_cmdline_in_header", -// 1, -// Arrays.asList("6c0b0c5f03d26f4a7a1438a2afc9fb6b") -// ); -// -// executeTest("testVariantTypeSelection--" + testFile, spec); -// } -// -// @Test -// public void testUsingDbsnpName() { -// String testFile = testDir + "combine.3.vcf"; -// -// WalkerTestSpec spec = new WalkerTestSpec( -// "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header", -// 1, -// Arrays.asList("a8a26c621018142c9cba1080cbe687a8") -// ); -// -// executeTest("testUsingDbsnpName--" + testFile, spec); -// } -// -// @Test -// public void testRegenotype() { -// String testFile = testDir + "combine.3.vcf"; -// -// WalkerTestSpec spec = new WalkerTestSpec( -// "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header", -// 1, -// Arrays.asList("6bee6dc2316aa539560a6d9d8adbc4ff") -// ); -// -// executeTest("testRegenotype--" + testFile, spec); -// } + @Test + public void testDiscordanceNoSampleSpecified() { + String testFile = testDir + "NA12878.hg19.example1.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header", + 1, + Arrays.asList("9fb54ed003234a5847c565ffb6767b95") + ); + spec.disableShadowBCF(); + + executeTest("testDiscordanceNoSampleSpecified--" + testFile, spec); + } + + @Test + public void testRepeatedLineSelection() { + String testfile = testDir + "test.dup.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString(" -sn A -sn B -sn C --variant " + testfile), + 1, + Arrays.asList("77579c53dbde4e8171f3cee83b98351b") + ); + + executeTest("testRepeatedLineSelection--" + testfile, spec); + } + + @Test + public void testDiscordance() { + String testFile = testDir + "NA12878.hg19.example1.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header", + 1, + Arrays.asList("03abdc27bfd7aa36d57bba0325b31e0d") + ); + spec.disableShadowBCF(); + + executeTest("testDiscordance--" + testFile, spec); + } + + @Test + public void testComplexSelection() { + String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; + String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; + + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile), + 1, + Arrays.asList("6cd82274335eeb0b449e571f38d54d3a") + ); + spec.disableShadowBCF(); + executeTest("testComplexSelection--" + testfile, spec); + } + + @Test + public void testSampleExclusion() { + String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; + String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sn A -xl_sf " + samplesFile + " --variant " + testfile, + 1, + Arrays.asList("bbd7b28d1c5701e17b395d64f8b6f13d") + ); + spec.disableShadowBCF(); + + executeTest("testSampleExclusion--" + testfile, spec); + } + + + @Test + public void testConcordance() { + String testFile = testDir + "NA12878.hg19.example1.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc " + b37hapmapGenotypes + " --variant " + testFile + " -o %s --no_cmdline_in_header", + 1, + Arrays.asList("76857b016198c3e08a2e27bbdb49f3f0") + ); + spec.disableShadowBCF(); + + executeTest("testConcordance--" + testFile, spec); + } + + @Test + public void testVariantTypeSelection() { + String testFile = testDir + "complexExample1.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s --no_cmdline_in_header", + 1, + Arrays.asList("6c0b0c5f03d26f4a7a1438a2afc9fb6b") + ); + + executeTest("testVariantTypeSelection--" + testFile, spec); + } + + @Test + public void testUsingDbsnpName() { + String testFile = testDir + "combine.3.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header", + 1, + Arrays.asList("a8a26c621018142c9cba1080cbe687a8") + ); + + executeTest("testUsingDbsnpName--" + testFile, spec); + } + + @Test + public void testRegenotype() { + String testFile = testDir + "combine.3.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header", + 1, + Arrays.asList("6bee6dc2316aa539560a6d9d8adbc4ff") + ); + + executeTest("testRegenotype--" + testFile, spec); + } @Test public void testMultipleRecordsAtOnePosition() { @@ -143,61 +144,61 @@ public class SelectVariantsIntegrationTest extends WalkerTest { Arrays.asList("6ff686a64e98fc1be2cde9b034d4a43a") ); - executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec); + executeTest("testMultipleRecordsAtOnePosition--" + testFile, spec); } -// @Test -// public void testNoGTs() { -// String testFile = testDir + "vcf4.1.example.vcf"; -// -// WalkerTestSpec spec = new WalkerTestSpec( -// "-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header", -// 1, -// Arrays.asList("95c4d43b11c3d0dd3ab19941c474269b") -// ); -// -// executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec); -// } -// -// @Test -// public void testParallelization2() { -// String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; -// String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; -// WalkerTestSpec spec; -// -// spec = new WalkerTestSpec( -// baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 2"), -// 1, -// Arrays.asList("6cd82274335eeb0b449e571f38d54d3a") -// ); -// spec.disableShadowBCF(); -// executeTest("testParallelization (2 threads)--" + testfile, spec); -// } -// -// @Test -// public void testParallelization4() { -// String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; -// String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; -// WalkerTestSpec spec; -// spec = new WalkerTestSpec( -// baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 4"), -// 1, -// Arrays.asList("6cd82274335eeb0b449e571f38d54d3a") -// ); -// spec.disableShadowBCF(); -// -// executeTest("testParallelization (4 threads)--" + testfile, spec); -// } -// -// @Test -// public void testSelectFromMultiAllelic() { -// String testfile = testDir + "multi-allelic.bi-allelicInGIH.vcf"; -// String samplesFile = testDir + "GIH.samples.list"; -// WalkerTestSpec spec = new WalkerTestSpec( -// "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile, -// 1, -// Arrays.asList("fa92b3b41f1c04f685be8de32afc9706") -// ); -// executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec); -// } + @Test + public void testNoGTs() { + String testFile = testDir + "vcf4.1.example.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header", + 1, + Arrays.asList("95c4d43b11c3d0dd3ab19941c474269b") + ); + + executeTest("testNoGTs--" + testFile, spec); + } + + @Test + public void testParallelization2() { + String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; + String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; + WalkerTestSpec spec; + + spec = new WalkerTestSpec( + baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 2"), + 1, + Arrays.asList("6cd82274335eeb0b449e571f38d54d3a") + ); + spec.disableShadowBCF(); + executeTest("testParallelization (2 threads)--" + testfile, spec); + } + + @Test + public void testParallelization4() { + String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; + String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; + WalkerTestSpec spec; + spec = new WalkerTestSpec( + baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 4"), + 1, + Arrays.asList("6cd82274335eeb0b449e571f38d54d3a") + ); + spec.disableShadowBCF(); + + executeTest("testParallelization (4 threads)--" + testfile, spec); + } + + @Test + public void testSelectFromMultiAllelic() { + String testfile = testDir + "multi-allelic.bi-allelicInGIH.vcf"; + String samplesFile = testDir + "GIH.samples.list"; + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile, + 1, + Arrays.asList("fa92b3b41f1c04f685be8de32afc9706") + ); + executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec); + } }