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Merge pull request #155 from broadinstitute/md_pnrm 

HaplotypeCaller doesn't support EXACT_GENERAL_PLOIDY model
This commit is contained in:
Mark DePristo 2013-04-09 12:20:55 -07:00
parent 55c9542bfd 51954ae3e5
commit 0194c9492d
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 */
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);
/**

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.UnifiedGenotyperEngine;
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.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
@ -366,6 +367,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
public void 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
Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
samplesList.addAll( samples );