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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2013-03-04 23:24:44 -05:00
parent 1b7164ccdb b715218bfe
commit bd4e4f4ee3
1 changed files with 15 additions and 4 deletions
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19
protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -343,8 +343,10 @@ public class PairHMMIndelErrorModel {
}
}
else {
final byte[] readBases = Arrays.copyOfRange(unclippedReadBases,numStartSoftClippedBases, unclippedReadBases.length-numEndSoftClippedBases);
final byte[] readQuals = Arrays.copyOfRange(unclippedReadQuals,numStartSoftClippedBases, unclippedReadBases.length-numEndSoftClippedBases);
final int endOfCopy = unclippedReadBases.length - numEndSoftClippedBases;
final byte[] readBases = Arrays.copyOfRange(unclippedReadBases, numStartSoftClippedBases, endOfCopy);
final byte[] readQuals = Arrays.copyOfRange(unclippedReadQuals, numStartSoftClippedBases, endOfCopy);
int j=0;
byte[] previousHaplotypeSeen = null;
@ -356,6 +358,16 @@ public class PairHMMIndelErrorModel {
getContextHomopolymerLength(readBases,hrunProfile);
fillGapProbabilities(hrunProfile, contextLogGapOpenProbabilities, contextLogGapContinuationProbabilities);
// get the base insertion and deletion qualities to use
final byte[] baseInsertionQualities, baseDeletionQualities;
if ( read.hasBaseIndelQualities() ) {
baseInsertionQualities = Arrays.copyOfRange(read.getBaseInsertionQualities(), numStartSoftClippedBases, endOfCopy);
baseDeletionQualities = Arrays.copyOfRange(read.getBaseDeletionQualities(), numStartSoftClippedBases, endOfCopy);
} else {
baseInsertionQualities = contextLogGapOpenProbabilities;
baseDeletionQualities = contextLogGapOpenProbabilities;
}
boolean firstHap = true;
for (Allele a: haplotypeMap.keySet()) {
@ -394,8 +406,7 @@ public class PairHMMIndelErrorModel {
previousHaplotypeSeen = haplotypeBases.clone();
readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals,
(read.hasBaseIndelQualities() ? read.getBaseInsertionQualities() : contextLogGapOpenProbabilities),
(read.hasBaseIndelQualities() ? read.getBaseDeletionQualities() : contextLogGapOpenProbabilities),
baseInsertionQualities, baseDeletionQualities,
contextLogGapContinuationProbabilities, startIndexInHaplotype, firstHap);