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Updating MD5s in HC and UG that changed due to new LIBS 

-- Resolved what was clearly a bug in UG (GGA mode was returning a neighboring, equivalent indel site that wasn't in input list.  Not ideal)
-- Trivial read count differences in HC
This commit is contained in:
Mark DePristo 2013-01-11 15:16:47 -05:00
parent f204908a94
commit 85b529cced
2 changed files with 4 additions and 4 deletions
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2
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -397,7 +397,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("b6c1d5cd28ff584c5f5037afef4e883a"));
Arrays.asList("23b7a37a64065cee53a80495c8717eea"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
}

6
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -67,7 +67,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "35c8425b44429ac7468c2cd26f8f5a42");
HCTest(CEUTRIO_BAM, "", "b8f7b741445ce6b6ea491c794ce75c17");
}
@Test
@ -79,7 +79,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@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");
"c679ae7f04bdfda896b5c046d35e043c");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
@ -123,7 +123,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("2e8e6313228b0387008437feae7f5469"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("8b1b8d1bd7feac1503fc4ffa6236cff7"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}