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Bug fix: AlleleCount stratification in VariantEval didn't support higher ploidy and was producing bad tables

This commit is contained in:
Guillermo del Angel 2012-09-21 20:48:12 -04:00
parent dcd31e654d
commit ab8fa8f359
2 changed files with 6 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
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@ -171,6 +171,9 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
@Argument(shortName="mvq", fullName="mendelianViolationQualThreshold", doc="Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50.", required=false)
protected double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 50;
@Argument(shortName="ploidy", fullName="samplePloidy", doc="Per-sample ploidy (number of chromosomes per sample)", required=false)
protected int ploidy = VariantContextUtils.DEFAULT_PLOIDY;
@Argument(fullName="ancestralAlignments", shortName="aa", doc="Fasta file with ancestral alleles", required=false)
private File ancestralAlignmentsFile = null;
@ -574,6 +577,7 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
public double getMinPhaseQuality() { return MIN_PHASE_QUALITY; }
public int getSamplePloidy() { return ploidy; }
public double getMendelianViolationQualThreshold() { return MENDELIAN_VIOLATION_QUAL_THRESHOLD; }
public static String getAllSampleName() { return ALL_SAMPLE_NAME; }

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
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@ -27,9 +27,9 @@ public class AlleleCount extends VariantStratifier {
if ( getVariantEvalWalker().getEvals().size() != 1 && !getVariantEvalWalker().mergeEvals )
throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification only works with a single eval vcf");
// There are 2 x n sample chromosomes for diploids
// There are ploidy x n sample chromosomes
// TODO -- generalize to handle multiple ploidy
nchrom = getVariantEvalWalker().getSampleNamesForEvaluation().size() * 2;
nchrom = getVariantEvalWalker().getSampleNamesForEvaluation().size() * getVariantEvalWalker().getSamplePloidy();
if ( nchrom < 2 )
throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification requires an eval vcf with at least one sample");