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Deprecate --mergeVariantsViaLD in HC 

New unit test for deprecated mergeVariantsViaLD
Update HaplotypeCallerIntegrationTest.java
Delete duplicate testHaplotypeCallerMergeVariantsViaLDException test.
This commit is contained in:
Joseph White 2015-04-26 17:32:08 -04:00 committed by Geraldine Van der Auwera
parent 8a4a4f3fcf
commit 5be8bc5dfc
2 changed files with 31 additions and 6 deletions
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23
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -387,11 +387,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
@Argument(fullName="useAllelesTrigger", shortName="allelesTrigger", doc = "Use additional trigger on variants found in an external alleles file", required=false)
protected boolean USE_ALLELES_TRIGGER = false;
@Advanced
@Argument(fullName="mergeVariantsViaLD", shortName="mergeVariantsViaLD", doc="Merge variants together into block substitutions if they are in strong local LD", required = false)
protected boolean mergeVariantsViaLD = false;
/**
* As of GATK 3.3, HaplotypeCaller outputs physical (read-based) information (see version 3.3 release notes and documentation for details). This argument disables that behavior.
*/
@ -495,6 +490,22 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
ReferenceConfidenceModel referenceConfidenceModel = null;
////////////////////////////////////////////////////////////////////////
//// Deprecated Arguments ////
//// Keeping them here is meant to provide informative error messages //
//// when an argument has been put out of service ////
////////////////////////////////////////////////////////////////////////
/**
* @deprecated
* Deprecated: 2015-04-01, J.White
* mergeVariantsViaLD = false made final
*/
@Hidden
@Deprecated
@Argument(fullName="mergeVariantsViaLD", shortName="mergeVariantsViaLD", doc="DEPRECATED; This argument is no longer used in GATK versions 3.4 and newer. Please see the online documentation for the latest usage recommendations.", required = false)
static final boolean mergeVariantsViaLD = false;
//---------------------------------------------------------------------------------------------------------------
//
// initialize
@ -654,7 +665,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
// create our likelihood calculation engine
likelihoodCalculationEngine = createLikelihoodCalculationEngine();
final MergeVariantsAcrossHaplotypes variantMerger = mergeVariantsViaLD ? new LDMerger(HCAC.DEBUG, 10, 1) : new MergeVariantsAcrossHaplotypes();
final MergeVariantsAcrossHaplotypes variantMerger = new MergeVariantsAcrossHaplotypes();
genotypingEngine.setCrossHaplotypeEventMerger(variantMerger);

14
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -444,8 +444,22 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
1, UserException.CommandLineException.class));
}
@Test
public void testHaplotypeCallerMergeVariantsViaLDException(){
executeTest("HaplotypeCallerMergeVariantsViaLDException",
new WalkerTest.WalkerTestSpec(
" -T HaplotypeCaller" +
" -R " + REF +
" -I " + NA12878_BAM +
" -L " + INTERVALS_FILE +
" --mergeVariantsViaLD " +
" -o %s",
1, UserException.DeprecatedArgument.class));
}
@Test
public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "481787c9275ab9f2e2b53025805472b7");
}
}