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Solve merge conflict

This commit is contained in:
Guillermo del Angel 2011-11-22 22:48:03 -05:00
parent a3aef8fa53 75d93e6335
commit 941f3784dc
1 changed files with 4 additions and 1 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -557,8 +557,11 @@ public class PairHMMIndelErrorModel {
long indStop = stop - haplotype.getStartPosition(); long indStop = stop - haplotype.getStartPosition();
double readLikelihood; double readLikelihood;
if (DEBUG)
System.out.format("indStart: %d indStop: %d WinStart:%d WinStop:%d start: %d stop: %d readLength: %d C:%s\n",
indStart, indStop, ref.getWindow().getStart(), ref.getWindow().getStop(), start, stop, read.getReadLength(), read.getCigar().toString());
if (indStart < 0 || indStop >= haplotype.getBases().length) { if (indStart < 0 || indStop >= haplotype.getBasesAsBytes().length || indStart > indStop) {
// read spanned more than allowed reference context: we currently can't deal with this // read spanned more than allowed reference context: we currently can't deal with this
readLikelihood =0; readLikelihood =0;
} else } else