zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fix contact on sorting of AFCalcResults 

-- The thing that must be sorted is the pre-theta^N list, which is not checked in the routine that applies the theta^N prior.
This commit is contained in:
Mark DePristo 2012-10-19 17:11:31 -04:00
parent eaffb814d3
commit 0fb8274507
1 changed files with 5 additions and 12 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

15
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
View File

@ -285,9 +285,13 @@ import java.util.*;
// sort the results, so the most likely allele is first // sort the results, so the most likely allele is first
Collections.sort(sorted, compareAFCalcResultsByPNonRef); Collections.sort(sorted, compareAFCalcResultsByPNonRef);
double lastPosteriorGt0 = sorted.get(0).getLog10PosteriorOfAFGT0();
final double log10SingleAllelePriorOfAFGt0 = conditionalPNonRefResults.get(0).getLog10PriorOfAFGT0(); final double log10SingleAllelePriorOfAFGt0 = conditionalPNonRefResults.get(0).getLog10PriorOfAFGT0();
for ( int i = 0; i < sorted.size(); i++ ) { for ( int i = 0; i < sorted.size(); i++ ) {
if ( sorted.get(i).getLog10PosteriorOfAFGT0() > lastPosteriorGt0 )
throw new IllegalStateException("pNonRefResults not sorted: lastPosteriorGt0 " + lastPosteriorGt0 + " but current is " + sorted.get(i).getLog10PosteriorOfAFGT0());
final double log10PriorAFGt0 = (i + 1) * log10SingleAllelePriorOfAFGt0; final double log10PriorAFGt0 = (i + 1) * log10SingleAllelePriorOfAFGt0;
final double log10PriorAFEq0 = Math.log10(1 - Math.pow(10, log10PriorAFGt0)); final double log10PriorAFEq0 = Math.log10(1 - Math.pow(10, log10PriorAFGt0));
final double[] thetaTONPriors = new double[] { log10PriorAFEq0, log10PriorAFGt0 }; final double[] thetaTONPriors = new double[] { log10PriorAFEq0, log10PriorAFGt0 };
@ -313,7 +317,6 @@ import java.util.*;
* *
* @param sortedResultsWithThetaNPriors the pNonRef result for each allele independently * @param sortedResultsWithThetaNPriors the pNonRef result for each allele independently
*/ */
@Requires("sortedByPosteriorGT(sortedResultsWithThetaNPriors)")
protected AFCalcResult combineIndependentPNonRefs(final VariantContext vc, protected AFCalcResult combineIndependentPNonRefs(final VariantContext vc,
final List<AFCalcResult> sortedResultsWithThetaNPriors) { final List<AFCalcResult> sortedResultsWithThetaNPriors) {
int nEvaluations = 0; int nEvaluations = 0;
@ -374,14 +377,4 @@ import java.util.*;
MathUtils.normalizeFromLog10(log10PriorsOfAC, true), MathUtils.normalizeFromLog10(log10PriorsOfAC, true),
log10pNonRefByAllele, sortedResultsWithThetaNPriors); log10pNonRefByAllele, sortedResultsWithThetaNPriors);
} }
private static boolean sortedByPosteriorGT(final List<AFCalcResult> sortedVCs) {
double lastPosteriorGt0 = sortedVCs.get(0).getLog10PosteriorOfAFGT0();
for ( final AFCalcResult vc : sortedVCs ) {
if ( vc.getLog10PosteriorOfAFGT0() > lastPosteriorGt0 )
return false;
lastPosteriorGt0 = vc.getLog10PosteriorOfAFGT0();
}
return true;
}
} }