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HaplotypeCaller doesn't support EXACT_GENERAL_PLOIDY model 

-- HC now throws a UserException if this model is provided.  Documented this option as not being supported in the HC in the docs for EXACT_GENERAL_PLOIDY
This commit is contained in:
Mark DePristo 2013-04-09 15:18:42 -04:00
parent 55c9542bfd
commit 51954ae3e5
2 changed files with 5 additions and 1 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
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@ -79,7 +79,7 @@ public class AFCalcFactory {
/** original biallelic exact model, for testing only */ /** original biallelic exact model, for testing only */
EXACT_ORIGINAL(OriginalDiploidExactAFCalc.class, 2, 2), EXACT_ORIGINAL(OriginalDiploidExactAFCalc.class, 2, 2),
/** implementation that supports any sample ploidy */ /** implementation that supports any sample ploidy. Currently not available for the HaplotypeCaller */
EXACT_GENERAL_PLOIDY("GeneralPloidyExactAFCalc", -1, -1); EXACT_GENERAL_PLOIDY("GeneralPloidyExactAFCalc", -1, -1);
/** /**

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -67,6 +67,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalcul
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion; import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState; import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
@ -366,6 +367,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
public void initialize() { public void initialize() {
super.initialize(); super.initialize();
if ( SCAC.AFmodel == AFCalcFactory.Calculation.EXACT_GENERAL_PLOIDY )
throw new UserException.BadArgumentValue("pnrm", "HaplotypeCaller doesn't currently support " + SCAC.AFmodel);
// get all of the unique sample names // get all of the unique sample names
Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()); Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
samplesList.addAll( samples ); samplesList.addAll( samples );