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Merged bug fix from Stable into Unstable

This commit is contained in:
Guillermo del Angel 2011-07-20 13:19:35 -04:00
parent c09f92ccee f15023b7d2
commit 0a1d2df8cb
2 changed files with 5 additions and 5 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -391,7 +391,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
if (DEBUG) if (DEBUG)
System.out.format("hsize: %d eventLength: %d refSize: %d, locStart: %d numpr: %d\n",hsize,eventLength, System.out.format("hsize: %d eventLength: %d refSize: %d, locStart: %d numpr: %d\n",hsize,eventLength,
(int)ref.getWindow().size(), loc.getStart(), numPrefBases); (int)ref.getWindow().size(), loc.getStart(), numPrefBases);
//System.out.println(eventLength);
haplotypeMap = Haplotype.makeHaplotypeListFromAlleles( alleleList, loc.getStart(), haplotypeMap = Haplotype.makeHaplotypeListFromAlleles( alleleList, loc.getStart(),
ref, hsize, numPrefBases); ref, hsize, numPrefBases);
@ -418,8 +418,8 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
// which genotype likelihoods correspond to two most likely alleles? By convention, likelihood vector is lexically ordered, for example // which genotype likelihoods correspond to two most likely alleles? By convention, likelihood vector is ordered as for example
// for 3 alleles it's 00 01 02 11 12 22 // for 3 alleles it's 00 01 11 02 12 22
GLs.put(sample.getKey(), new MultiallelicGenotypeLikelihoods(sample.getKey(), GLs.put(sample.getKey(), new MultiallelicGenotypeLikelihoods(sample.getKey(),
alleleList, alleleList,
genotypeLikelihoods, genotypeLikelihoods,

4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -1042,8 +1042,8 @@ public class PairHMMIndelErrorModel {
int k=0; int k=0;
double maxElement = Double.NEGATIVE_INFINITY; double maxElement = Double.NEGATIVE_INFINITY;
for (int i=0; i < hSize; i++) { for (int j=0; j < hSize; j++) {
for (int j=i; j < hSize; j++){ for (int i=0; i <= j; i++){
genotypeLikelihoods[k++] = haplotypeLikehoodMatrix[i][j]; genotypeLikelihoods[k++] = haplotypeLikehoodMatrix[i][j];
if (haplotypeLikehoodMatrix[i][j] > maxElement) if (haplotypeLikehoodMatrix[i][j] > maxElement)
maxElement = haplotypeLikehoodMatrix[i][j]; maxElement = haplotypeLikehoodMatrix[i][j];