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It was possible that we'd clean up a matrix column too early when a dependent column aborted early (with not enough probability mass) because we weren't being smart about the order in which we created dependencies. Fixed.

This commit is contained in:
Eric Banks 2012-01-25 14:28:21 -05:00
parent 2799a1b686
commit 05816955aa
1 changed files with 45 additions and 34 deletions
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17
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.sting.utils.variantcontext.*;
import java.io.PrintStream; import java.io.PrintStream;
@ -256,14 +255,24 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
// add conformations for the k+2 case if it makes sense; note that the 2 new alleles may be the same or different // add conformations for the k+2 case if it makes sense; note that the 2 new alleles may be the same or different
if ( ACwiggle > 1 ) { if ( ACwiggle > 1 ) {
for ( int allele_i = 0; allele_i < numAltAlleles; allele_i++ ) { // IMPORTANT: we must first add the cases where the 2 new alleles are different so that the queue maintains its ordering
for ( int allele_j = allele_i; allele_j < numAltAlleles; allele_j++ ) { for ( int allele_i = 0; allele_i < numAltAlleles - 1; allele_i++ ) {
for ( int allele_j = allele_i + 1; allele_j < numAltAlleles; allele_j++ ) {
if ( allele_i == allele_j )
continue;
final int[] ACcountsClone = set.ACcounts.getCounts().clone(); final int[] ACcountsClone = set.ACcounts.getCounts().clone();
ACcountsClone[allele_i]++; ACcountsClone[allele_i]++;
ACcountsClone[allele_j]++; ACcountsClone[allele_j]++;
lastSet = updateACset(ACcountsClone, numChr, set, ++PLindex , ACqueue, indexesToACset); lastSet = updateACset(ACcountsClone, numChr, set, ++PLindex , ACqueue, indexesToACset);
} }
} }
// now we can deal with the case where the 2 new alleles are the same
for ( int allele_i = 0; allele_i < numAltAlleles; allele_i++ ) {
final int[] ACcountsClone = set.ACcounts.getCounts().clone();
ACcountsClone[allele_i] += 2;
lastSet = updateACset(ACcountsClone, numChr, set, ++PLindex , ACqueue, indexesToACset);
}
} }
// if the last dependent set was not at the back of the queue (i.e. not just added), then we need to iterate // if the last dependent set was not at the back of the queue (i.e. not just added), then we need to iterate
@ -298,6 +307,8 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
} }
// add the given dependency to the set // add the given dependency to the set
//if ( DEBUG )
// System.out.println(" *** adding dependency from " + index + " to " + callingSet.ACcounts);
final ExactACset set = indexesToACset.get(index); final ExactACset set = indexesToACset.get(index);
set.ACsetIndexToPLIndex.put(callingSet.ACcounts, PLsetIndex); set.ACsetIndexToPLIndex.put(callingSet.ACcounts, PLsetIndex);
return wasInQueue ? null : set; return wasInQueue ? null : set;