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Merge pull request #136 from broadinstitute/gda_leftalign_fix 

Big bad bug fix: feature added to LeftAlignAndTrimVariants to left align...
This commit is contained in:
Eric Banks 2013-03-30 18:23:39 -07:00
parent f42bdaee3c 6b8bed34d0
commit baf5240e2b
2 changed files with 22 additions and 8 deletions
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10
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
View File

@ -64,4 +64,14 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
Arrays.asList("bcf05f56adbb32a47b6d6b27b327d5c2")); Arrays.asList("bcf05f56adbb32a47b6d6b27b327d5c2"));
executeTest("test left alignment", spec); executeTest("test left alignment", spec);
} }
@Test
public void testLeftAlignmentWithTrimmingAndMultialleliecs() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --no_cmdline_in_header -trim -split",
1,
Arrays.asList("4ae03954f8bd66e73fd005c49ea301db"));
executeTest("test left alignment with trimming and hard multiple alleles", spec);
}
} }

12
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java
View File

@ -138,18 +138,22 @@ public class LeftAlignAndTrimVariants extends RodWalker<Integer, Integer> {
if (splitMultiallelics) { if (splitMultiallelics) {
final List<VariantContext> vcList = GATKVariantContextUtils.splitVariantContextToBiallelics( vc); final List<VariantContext> vcList = GATKVariantContextUtils.splitVariantContextToBiallelics( vc);
for (final VariantContext biallelicVC: vcList) { for (final VariantContext biallelicVC: vcList) {
final VariantContext v = (trimAlleles ? GATKVariantContextUtils.trimAlleles(vc,true,true):biallelicVC); final VariantContext v = (trimAlleles ? GATKVariantContextUtils.trimAlleles(biallelicVC,true,true):biallelicVC);
result = alignAndWrite(v, ref); result = alignAndWrite(v, ref);
writer.add(result.first);
changedSites += result.second;
} }
} }
else if (trimAlleles) else {
if (trimAlleles)
result = alignAndWrite(GATKVariantContextUtils.trimAlleles(vc,true,true), ref); result = alignAndWrite(GATKVariantContextUtils.trimAlleles(vc,true,true), ref);
else else
result = alignAndWrite(vc,ref); result = alignAndWrite(vc,ref);
writer.add(result.first); writer.add(result.first);
changedSites += result.second; changedSites += result.second;
}
} }
return changedSites; return changedSites;