diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index e7f89bf08..ae419a5c4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -156,7 +156,7 @@ public class UnifiedArgumentCollection { public boolean OUTPUT_DEBUG_INDEL_INFO = false; @Hidden - @Argument(fullName = "dovit", shortName = "dovit", doc = "Output indel debug info", required = false) + @Argument(fullName = "dovit", shortName = "dovit", doc = "Perform full Viterbi calculation when evaluating the HMM", required = false) public boolean dovit = false; @Hidden diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index 55450486b..2d7969230 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -274,7 +274,7 @@ public class PairHMMIndelErrorModel { this.doViterbi = dovit; } - public PairHMMIndelErrorModel(double indelGOP, double indelGCP, boolean deb, boolean doCDP) { + public PairHMMIndelErrorModel(double indelGOP, double indelGCP, boolean deb, boolean doCDP) { this.logGapOpenProbability = -indelGOP/10.0; // QUAL to log prob @@ -754,7 +754,7 @@ public class PairHMMIndelErrorModel { // check if we've already computed likelihoods for this pileup element (i.e. for this read at this location) if (indelLikelihoodMap.containsKey(p)) { - HashMap el = indelLikelihoodMap.get(p); + HashMap el = indelLikelihoodMap.get(p); int j=0; for (Allele a: haplotypeMap.keySet()) { readLikelihoods[readIdx][j++] = el.get(a); @@ -1055,7 +1055,6 @@ public class PairHMMIndelErrorModel { genotypeLikelihoods[i] -= maxElement; return genotypeLikelihoods; - } /**