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Decrease interval on CGP integration test to reduce test execution time

This commit is contained in:
Laura Gauthier 2014-10-15 11:18:01 -04:00
parent 0ad9daeac1
commit 81482138ca
1 changed files with 7 additions and 4 deletions
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11
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java
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@ -63,28 +63,31 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
private static String CEUtrioPopPriorsTest = privateTestDir + "CEUtrioPopPriorsTest.vcf"; private static String CEUtrioPopPriorsTest = privateTestDir + "CEUtrioPopPriorsTest.vcf";
@Test(enabled = true) @Test(enabled = true)
//use the first 20 variants to save time; they have a nice range of AC from 4 to over 4000
public void testUsingDiscoveredAF() { public void testUsingDiscoveredAF() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
"-T CalculateGenotypePosteriors --no_cmdline_in_header" + "-T CalculateGenotypePosteriors --no_cmdline_in_header" +
" -o %s" + " -o %s" +
" -R " + b37KGReference + " -R " + b37KGReference +
" -L 20:10,000,000-10,100,000" + " -L 20:10,000,000-10,001,432" +
" -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf", " -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf",
1, 1,
Arrays.asList("75c4b1baba3071047e4629c8e81ddea1")); Arrays.asList("afe5c06ef62612e4c663a3f8e9f5cd60"));
executeTest("testUsingDiscoveredAF", spec); executeTest("testUsingDiscoveredAF", spec);
} }
@Test(enabled = true) @Test(enabled = true)
//this test ignores discovered AC and has no external priors, so it should only apply the PP tag with values the same as PLs
//only test the first 20 variants to save time
public void testMissingPriors() { public void testMissingPriors() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
"-T CalculateGenotypePosteriors --no_cmdline_in_header -useACoff" + "-T CalculateGenotypePosteriors --no_cmdline_in_header -useACoff" +
" -o %s" + " -o %s" +
" -R " + b37KGReference + " -R " + b37KGReference +
" -L 20:10,000,000-10,100,000" + " -L 20:10,000,000-10,001,432" +
" -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf", " -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf",
1, 1,
Arrays.asList("5a2d7481fc69b97033f8c3ae9c0bdd20")); Arrays.asList("de153b79fd1c0e1c1f769ec4a9fb01e0"));
executeTest("testMissingPriors", spec); executeTest("testMissingPriors", spec);
} }