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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mark DePristo 2011-11-23 13:02:11 -05:00
parent 4107636144 e5b85f0a78
commit e319079c32
2 changed files with 8 additions and 1 deletions
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4
public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
View File

@ -108,4 +108,8 @@ public final class IntervalBinding<T extends Feature> {
return intervals;
}
public String toString() {
return getSource();
}
}

5
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
View File

@ -557,8 +557,11 @@ public class PairHMMIndelErrorModel {
long indStop = stop - haplotype.getStartPosition();
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.getBases().length || indStart > indStop) {
// read spanned more than allowed reference context: we currently can't deal with this
readLikelihood =0;
} else