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Have CombineVariants throw a UserError when trying to combine GVCFs from the HaplotypeCaller. 

Was previously throwing an IllegalArgumentException (in the wrong place in the code).
Error message tells users to use CombineGVCFs.
This commit is contained in:
Eric Banks 2014-03-19 19:11:40 -04:00
parent 7117bebb5e
commit 3b1c337401
3 changed files with 16 additions and 4 deletions
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13
protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -204,4 +204,17 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
Arrays.asList("f8c014d0af7e014475a2a448dc1f9cef"));
cvExecuteTest("combineLeavesUnfilteredRecordsUnfiltered: ", spec, false);
}
@Test
public void combiningGVCFsFails() {
try {
WalkerTestSpec spec = new WalkerTestSpec(
"-T CombineVariants --no_cmdline_in_header -o %s "
+ " -R " + b37KGReference
+ " -V " + privateTestDir + "gvcfExample1.vcf",
1,
Arrays.asList("FAILFAILFAILFAILFAILFAILFAILFAIL"));
executeTest("combiningGVCFsFails", spec);
} catch (Exception e) { } // do nothing
}
}

3
public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -326,6 +326,9 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
if ( mergedVC == null )
continue;
if ( mergedVC.hasAllele(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE) )
throw new UserException("CombineVariants should not be used to merge gVCFs produced by the HaplotypeCaller; use CombineGVCFs instead");
final VariantContextBuilder builder = new VariantContextBuilder(mergedVC);
// re-compute chromosome counts
VariantContextUtils.calculateChromosomeCounts(builder, false);

4
public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
View File

@ -1921,10 +1921,6 @@ public class GATKVariantContextUtils {
final HashMap<VariantContext.Type, List<VariantContext>> mappedVCs = new HashMap<>();
for ( final VariantContext vc : VCs ) {
VariantContext.Type vcType = vc.getType();
if( vc.hasAllele(NON_REF_SYMBOLIC_ALLELE) ) {
if( vc.getAlternateAlleles().size() > 1 ) { throw new IllegalStateException("Reference records should not have more than one alternate allele"); }
vcType = VariantContext.Type.NO_VARIATION;
}
// look at previous variant contexts of different type. If:
// a) otherVC has alleles which are subset of vc, remove otherVC from its list and add otherVC to vc's list