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Adding additional HC GGA integration tests to cover more complicated input alleles.

This commit is contained in:
Ryan Poplin 2013-01-11 14:36:21 -05:00
parent bc64d4240f
commit 7f7f40f851
1 changed files with 18 additions and 1 deletions
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19
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -75,13 +75,30 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
HCTest(NA12878_BAM, "", "a2c63f6e6e51a01019bdbd23125bdb15");
}
// TODO -- add more tests for GGA mode, especially with input alleles that are complex variants and/or not trimmed
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
"d918d25b22a551cae5d70ea30d7feed1");
}
private void HCTestComplexGGA(String bam, String args, String md5) {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " --no_cmdline_in_header -o %s -minPruning 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
executeTest("testHaplotypeCallerComplexGGA: args=" + args, spec);
}
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(CEUTRIO_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"aaaad25b22a551cae5d70ea30d7feed1");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(CEUTRIO_BAM, "-L 20:133041-133161",
"bbbbd25b22a551cae5d70ea30d7feed1");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " -L 20:10028767-10028967 -L 20:10431524-10431924 -L 20:10723661-10724061 -L 20:10903555-10903955 --no_cmdline_in_header -o %s -minPruning 4";
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));