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

Minor improvements to CombineVariants to handle the complex case from Chris. IntegrationTest of complex case. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3876 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-07-25 13:46:11 +00:00
parent 7c5a3836db
commit 19ad44d332
2 changed files with 18 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
View File

@ -301,6 +301,8 @@ public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs,
setValue = "Intersection";
else if ( nFiltered == VCs.size() ) // everything was filtered out
setValue = "FilteredInAll";
else if ( nVariant == 0 ) // everyone was reference
setValue = "ReferenceInAll";
else { // we are filtered in some subset
List<String> s = new ArrayList<String>();
for ( VariantContext vc : VCs )

16
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -74,4 +74,20 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "a66a799b1ae9fd09b40f78af6ef538d8"); }
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "a9126d1cbe1fdf741236763fb3e3461f"); }
@Test public void threeWayWithRefs() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -B NA19240_BGI,VCF4,"+validationDataLocation+"NA19240.BGI.RG.vcf" +
" -B NA19240_ILLUMINA,VCF4,"+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
" -B NA19240_WUGSC,VCF4,"+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
" -B denovoInfo,VCF,"+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
" -setKey centerSet" +
" -variantMergeOptions UNION" +
" -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
" -genotypeMergeOptions UNIQUIFY -L 1"),
1,
Arrays.asList("37c66ca16fb5f890bcaa8e226a5f2e61"));
executeTest("threeWayWithRefs", spec);
}
}