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Prevent out of bound error in case read span > reference context + indel length. Can happen in RNAseq reads with long N CIGAR operators in the middle.

This commit is contained in:
Guillermo del Angel 2011-11-22 13:57:24 -05:00
parent c62082ba1b
commit 32a77a8a56
1 changed files with 38 additions and 31 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -555,11 +555,16 @@ public class PairHMMIndelErrorModel {
// cut haplotype bases // cut haplotype bases
long indStart = start - haplotype.getStartPosition(); long indStart = start - haplotype.getStartPosition();
long indStop = stop - haplotype.getStartPosition(); long indStop = stop - haplotype.getStartPosition();
double readLikelihood;
if (indStart < 0 || indStop >= haplotype.getBasesAsBytes().length) {
// read spanned more than allowed reference context: we currently can't deal with this
readLikelihood =0;
} else
{
final byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBasesAsBytes(), final byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBasesAsBytes(),
(int)indStart, (int)indStop); (int)indStart, (int)indStop);
double readLikelihood;
if (matchMetricArray == null) { if (matchMetricArray == null) {
final int X_METRIC_LENGTH = readBases.length+1; final int X_METRIC_LENGTH = readBases.length+1;
final int Y_METRIC_LENGTH = haplotypeBases.length+1; final int Y_METRIC_LENGTH = haplotypeBases.length+1;
@ -585,12 +590,14 @@ public class PairHMMIndelErrorModel {
readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals, readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals,
currentContextGOP, currentContextGCP, startIdx, matchMetricArray, XMetricArray, YMetricArray); currentContextGOP, currentContextGCP, startIdx, matchMetricArray, XMetricArray, YMetricArray);
if (DEBUG) { if (DEBUG) {
System.out.println("H:"+new String(haplotypeBases)); System.out.println("H:"+new String(haplotypeBases));
System.out.println("R:"+new String(readBases)); System.out.println("R:"+new String(readBases));
System.out.format("L:%4.2f\n",readLikelihood); System.out.format("L:%4.2f\n",readLikelihood);
System.out.format("StPos:%d\n", startIdx); System.out.format("StPos:%d\n", startIdx);
} }
}
readEl.put(a,readLikelihood); readEl.put(a,readLikelihood);
readLikelihoods[readIdx][j++] = readLikelihood; readLikelihoods[readIdx][j++] = readLikelihood;
} }