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Enabling Fisher Strand for multi-allelics: use the alt allele with max AC. Added minor optimization to the method in the VC.

This commit is contained in:
Eric Banks 2012-02-27 09:50:09 -05:00
parent d34f07dba0
commit dfdf4f989b
2 changed files with 15 additions and 9 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -59,10 +59,10 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
int[][] table; int[][] table;
if (vc.isBiallelic() && vc.isSNP()) if ( vc.isSNP() )
table = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAlternateAllele(0)); table = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount());
else if (vc.isIndel() || vc.isMixed()) { else if ( vc.isIndel() || vc.isMixed() ) {
table = getIndelContingencyTable(stratifiedContexts, vc); table = getIndelContingencyTable(stratifiedContexts);
if (table == null) if (table == null)
return null; return null;
} }
@ -234,7 +234,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
* allele2 # # * allele2 # #
* @return a 2x2 contingency table * @return a 2x2 contingency table
*/ */
private static int[][] getIndelContingencyTable(Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) { private static int[][] getIndelContingencyTable(Map<String, AlignmentContext> stratifiedContexts) {
final double INDEL_LIKELIHOOD_THRESH = 0.3; final double INDEL_LIKELIHOOD_THRESH = 0.3;
final HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap = IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap(); final HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap = IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap();

14
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
View File

@ -1229,12 +1229,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
} }
public Allele getAltAlleleWithHighestAlleleCount() { public Allele getAltAlleleWithHighestAlleleCount() {
// first idea: get two alleles with highest AC // optimization: for bi-allelic sites, just return the 1only alt allele
if ( isBiallelic() )
return getAlternateAllele(0);
Allele best = null; Allele best = null;
int maxAC1 = 0; int maxAC1 = 0;
for (Allele a:this.getAlternateAlleles()) { for ( Allele a : getAlternateAlleles() ) {
int ac = this.getCalledChrCount(a); final int ac = getCalledChrCount(a);
if (ac >=maxAC1) { if ( ac >= maxAC1 ) {
maxAC1 = ac; maxAC1 = ac;
best = a; best = a;
} }
@ -1244,6 +1247,9 @@ public class VariantContext implements Feature { // to enable tribble intergrati
} }
public int[] getGLIndecesOfAllele(Allele inputAllele) { public int[] getGLIndecesOfAllele(Allele inputAllele) {
// TODO -- this information is cached statically by the UnifiedGenotyperEngine; pull it out into a common utils class for all to use
int[] idxVector = new int[3]; int[] idxVector = new int[3];
int numAlleles = this.getAlleles().size(); int numAlleles = this.getAlleles().size();