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New debug option to output the assembly graph in dot format. Merge nodes in assembly graph when possible.

This commit is contained in:
Ryan Poplin 2012-03-21 15:48:55 -04:00
parent 9e10779fa7
commit a29fc6311a
2 changed files with 2 additions and 2 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -500,7 +500,7 @@ public class PairHMMIndelErrorModel {
if (stop > ref.getWindow().getStop()) if (stop > ref.getWindow().getStop())
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 // but we want to compute likelihoods in the whole region that a read might overlap
if (stop <= start + readLength) { if (stop <= start + readLength) {
stop = start + readLength-1; stop = start + readLength-1;

2
public/java/src/org/broadinstitute/sting/utils/MathUtils.java
View File

@ -205,7 +205,7 @@ public class MathUtils {
/** /**
* Calculates the log10 cumulative sum of an array with log10 probabilities * 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 * @param upTo index in the array to calculate the cumsum up to
* @return the log10 of the cumulative sum * @return the log10 of the cumulative sum
*/ */