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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mauricio Carneiro 2011-10-21 17:45:07 -04:00
parent 86305a5dcf f4b409fa0d
commit 4913f8a60f
2 changed files with 5 additions and 3 deletions
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4
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
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@ -607,7 +607,7 @@ public class VariantContextUtils {
} }
// if we have more alternate alleles in the merged VC than in one or more of the // if we have more alternate alleles in the merged VC than in one or more of the
// original VCs, we need to strip out the GL/PLs (because they are no longer accurate) // original VCs, we need to strip out the GL/PLs (because they are no longer accurate), as well as allele-dependent attributes like AC,AF
for ( VariantContext vc : VCs ) { for ( VariantContext vc : VCs ) {
if (vc.alleles.size() == 1) if (vc.alleles.size() == 1)
continue; continue;
@ -615,6 +615,8 @@ public class VariantContextUtils {
logger.warn(String.format("Stripping PLs at %s due incompatible alleles merged=%s vs. single=%s", logger.warn(String.format("Stripping PLs at %s due incompatible alleles merged=%s vs. single=%s",
genomeLocParser.createGenomeLoc(vc), alleles, vc.alleles)); genomeLocParser.createGenomeLoc(vc), alleles, vc.alleles));
genotypes = stripPLs(genotypes); genotypes = stripPLs(genotypes);
// this will remove stale AC,AF attributed from vc
calculateChromosomeCounts(vc, attributes, true);
break; break;
} }
} }

4
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -96,8 +96,8 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "78a49597f1abf1c738e67d50c8fbed2b"); } @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "78a49597f1abf1c738e67d50c8fbed2b"); }
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "9253d61ddb52c429adf0e153cef494ca"); } @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "4c63bfa5f73793aaca42e130ec49f238"); }
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "5012dfe65cf7e7d8f014e97e4a996aea"); } @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "86e326acbd8d2af8a6040eb146d92fc6"); }
@Test public void threeWayWithRefs() { @Test public void threeWayWithRefs() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(