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Restoring SelectVariantsIntegrationTest

This commit is contained in:
Mark DePristo 2012-06-06 14:10:35 -04:00
parent 01ddf9555a
commit 6cfb2d1393
1 changed files with 178 additions and 177 deletions
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355
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
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@ -10,128 +10,129 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s --no_cmdline_in_header" + args; return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s --no_cmdline_in_header" + args;
} }
// @Test @Test
// public void testComplexSelection() { public void testDiscordanceNoSampleSpecified() {
// String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; String testFile = testDir + "NA12878.hg19.example1.vcf";
// String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
// WalkerTestSpec spec = new WalkerTestSpec(
// WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header",
// baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile), 1,
// 1, Arrays.asList("9fb54ed003234a5847c565ffb6767b95")
// Arrays.asList("6cd82274335eeb0b449e571f38d54d3a") );
// ); spec.disableShadowBCF();
// spec.disableShadowBCF();
// executeTest("testComplexSelection--" + testfile, spec); executeTest("testDiscordanceNoSampleSpecified--" + testFile, spec);
// } }
//
// @Test @Test
// public void testSampleExclusion() { public void testRepeatedLineSelection() {
// String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; String testfile = testDir + "test.dup.vcf";
// String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
// WalkerTestSpec spec = new WalkerTestSpec(
// WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -sn A -sn B -sn C --variant " + testfile),
// "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sn A -xl_sf " + samplesFile + " --variant " + testfile, 1,
// 1, Arrays.asList("77579c53dbde4e8171f3cee83b98351b")
// Arrays.asList("bbd7b28d1c5701e17b395d64f8b6f13d") );
// );
// spec.disableShadowBCF(); executeTest("testRepeatedLineSelection--" + testfile, spec);
// }
// executeTest("testSampleExclusion--" + testfile, spec);
// } @Test
// public void testDiscordance() {
// @Test String testFile = testDir + "NA12878.hg19.example1.vcf";
// public void testRepeatedLineSelection() {
// String testfile = testDir + "test.dup.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",
// WalkerTestSpec spec = new WalkerTestSpec( 1,
// baseTestString(" -sn A -sn B -sn C --variant " + testfile), Arrays.asList("03abdc27bfd7aa36d57bba0325b31e0d")
// 1, );
// Arrays.asList("77579c53dbde4e8171f3cee83b98351b") spec.disableShadowBCF();
// );
// executeTest("testDiscordance--" + testFile, spec);
// executeTest("testRepeatedLineSelection--" + testfile, spec); }
// }
// @Test
// @Test public void testComplexSelection() {
// public void testDiscordance() { String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
// String testFile = testDir + "NA12878.hg19.example1.vcf"; String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
//
// WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
// "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header", baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile),
// 1, 1,
// Arrays.asList("03abdc27bfd7aa36d57bba0325b31e0d") Arrays.asList("6cd82274335eeb0b449e571f38d54d3a")
// ); );
// spec.disableShadowBCF(); spec.disableShadowBCF();
// executeTest("testComplexSelection--" + testfile, spec);
// executeTest("testDiscordance--" + testFile, spec); }
// }
// @Test
// @Test public void testSampleExclusion() {
// public void testDiscordanceNoSampleSpecified() { String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
// String testFile = testDir + "NA12878.hg19.example1.vcf"; String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
//
// WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
// "-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header", "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sn A -xl_sf " + samplesFile + " --variant " + testfile,
// 1, 1,
// Arrays.asList("9fb54ed003234a5847c565ffb6767b95") Arrays.asList("bbd7b28d1c5701e17b395d64f8b6f13d")
// ); );
// spec.disableShadowBCF(); spec.disableShadowBCF();
//
// executeTest("testDiscordanceNoSampleSpecified--" + testFile, spec); executeTest("testSampleExclusion--" + testfile, spec);
// } }
//
// @Test
// public void testConcordance() { @Test
// String testFile = testDir + "NA12878.hg19.example1.vcf"; 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", WalkerTestSpec spec = new WalkerTestSpec(
// 1, "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc " + b37hapmapGenotypes + " --variant " + testFile + " -o %s --no_cmdline_in_header",
// Arrays.asList("76857b016198c3e08a2e27bbdb49f3f0") 1,
// ); Arrays.asList("76857b016198c3e08a2e27bbdb49f3f0")
// spec.disableShadowBCF(); );
// spec.disableShadowBCF();
// executeTest("testConcordance--" + testFile, spec);
// } executeTest("testConcordance--" + testFile, spec);
// }
// @Test
// public void testVariantTypeSelection() { @Test
// String testFile = testDir + "complexExample1.vcf"; 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", WalkerTestSpec spec = new WalkerTestSpec(
// 1, "-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s --no_cmdline_in_header",
// Arrays.asList("6c0b0c5f03d26f4a7a1438a2afc9fb6b") 1,
// ); Arrays.asList("6c0b0c5f03d26f4a7a1438a2afc9fb6b")
// );
// executeTest("testVariantTypeSelection--" + testFile, spec);
// } executeTest("testVariantTypeSelection--" + testFile, spec);
// }
// @Test
// public void testUsingDbsnpName() { @Test
// String testFile = testDir + "combine.3.vcf"; 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", WalkerTestSpec spec = new WalkerTestSpec(
// 1, "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header",
// Arrays.asList("a8a26c621018142c9cba1080cbe687a8") 1,
// ); Arrays.asList("a8a26c621018142c9cba1080cbe687a8")
// );
// executeTest("testUsingDbsnpName--" + testFile, spec);
// } executeTest("testUsingDbsnpName--" + testFile, spec);
// }
// @Test
// public void testRegenotype() { @Test
// String testFile = testDir + "combine.3.vcf"; 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", WalkerTestSpec spec = new WalkerTestSpec(
// 1, "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
// Arrays.asList("6bee6dc2316aa539560a6d9d8adbc4ff") 1,
// ); Arrays.asList("6bee6dc2316aa539560a6d9d8adbc4ff")
// );
// executeTest("testRegenotype--" + testFile, spec);
// } executeTest("testRegenotype--" + testFile, spec);
}
@Test @Test
public void testMultipleRecordsAtOnePosition() { public void testMultipleRecordsAtOnePosition() {
@ -143,61 +144,61 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
Arrays.asList("6ff686a64e98fc1be2cde9b034d4a43a") Arrays.asList("6ff686a64e98fc1be2cde9b034d4a43a")
); );
executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec); executeTest("testMultipleRecordsAtOnePosition--" + testFile, spec);
} }
// @Test @Test
// public void testNoGTs() { public void testNoGTs() {
// String testFile = testDir + "vcf4.1.example.vcf"; String testFile = testDir + "vcf4.1.example.vcf";
//
// WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
// "-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header", "-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
// 1, 1,
// Arrays.asList("95c4d43b11c3d0dd3ab19941c474269b") Arrays.asList("95c4d43b11c3d0dd3ab19941c474269b")
// ); );
//
// executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec); executeTest("testNoGTs--" + testFile, spec);
// } }
//
// @Test @Test
// public void testParallelization2() { public void testParallelization2() {
// String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
// String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
// WalkerTestSpec spec; WalkerTestSpec spec;
//
// spec = new WalkerTestSpec( spec = new WalkerTestSpec(
// baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 2"), baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 2"),
// 1, 1,
// Arrays.asList("6cd82274335eeb0b449e571f38d54d3a") Arrays.asList("6cd82274335eeb0b449e571f38d54d3a")
// ); );
// spec.disableShadowBCF(); spec.disableShadowBCF();
// executeTest("testParallelization (2 threads)--" + testfile, spec); executeTest("testParallelization (2 threads)--" + testfile, spec);
// } }
//
// @Test @Test
// public void testParallelization4() { public void testParallelization4() {
// String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
// String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
// WalkerTestSpec spec; WalkerTestSpec spec;
// spec = new WalkerTestSpec( spec = new WalkerTestSpec(
// baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 4"), baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 4"),
// 1, 1,
// Arrays.asList("6cd82274335eeb0b449e571f38d54d3a") Arrays.asList("6cd82274335eeb0b449e571f38d54d3a")
// ); );
// spec.disableShadowBCF(); spec.disableShadowBCF();
//
// executeTest("testParallelization (4 threads)--" + testfile, spec); executeTest("testParallelization (4 threads)--" + testfile, spec);
// } }
//
// @Test @Test
// public void testSelectFromMultiAllelic() { public void testSelectFromMultiAllelic() {
// String testfile = testDir + "multi-allelic.bi-allelicInGIH.vcf"; String testfile = testDir + "multi-allelic.bi-allelicInGIH.vcf";
// String samplesFile = testDir + "GIH.samples.list"; String samplesFile = testDir + "GIH.samples.list";
// WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
// "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile, "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile,
// 1, 1,
// Arrays.asList("fa92b3b41f1c04f685be8de32afc9706") Arrays.asList("fa92b3b41f1c04f685be8de32afc9706")
// ); );
// executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec); executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
// } }
} }