zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

355
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -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);
}
}