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 64993b43a..890ed9e3d 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 @@ -500,7 +500,7 @@ public class PairHMMIndelErrorModel { if (stop > ref.getWindow().getStop()) stop = ref.getWindow().getStop(); - // if there's an insertion in the read, the read stop position will be less than start + read legnth, + // if there's an insertion in the read, the read stop position will be less than start + read length, // but we want to compute likelihoods in the whole region that a read might overlap if (stop <= start + readLength) { stop = start + readLength-1; diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java index bfc326d2d..780eb2101 100644 --- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java @@ -205,7 +205,7 @@ public class MathUtils { /** * Calculates the log10 cumulative sum of an array with log10 probabilities * - * @param log10p the array with log10 probabilites + * @param log10p the array with log10 probabilities * @param upTo index in the array to calculate the cumsum up to * @return the log10 of the cumulative sum */