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

Another fix for genotype given alleles for indels. Expanding the indel integration tests to include multiallelics and indel records that overlap

This commit is contained in:
Ryan Poplin 2011-09-08 09:25:13 -04:00
parent e0020b2b29
commit 9cba1019c8
2 changed files with 4 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -321,7 +321,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
haplotypeMap.clear(); haplotypeMap.clear();
if (getAlleleListFromVCF) { if (getAlleleListFromVCF) {
for( final VariantContext vc_input : tracker.getValues(UAC.alleles) ) { for( final VariantContext vc_input : tracker.getValues(UAC.alleles, loc) ) {
if( vc_input != null && if( vc_input != null &&
allowableTypes.contains(vc_input.getType()) && allowableTypes.contains(vc_input.getType()) &&
ref.getLocus().getStart() == vc_input.getStart()) { ref.getLocus().getStart() == vc_input.getStart()) {

6
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -271,9 +271,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1,
Arrays.asList("408d3aba4d094c067fc00a43992c2292")); Arrays.asList("e66b7321e2ac91742ad3ef91040daafd"));
executeTest("test MultiSample Pilot2 indels with complicated records", spec3); executeTest("test MultiSample Pilot2 indels with complicated records", spec3);
} }