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Some changes regarding what to do when a cycle is completely busted. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@946 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-09 01:01:13 +00:00
parent 0bd78d72d7
commit 65d0675a4e
1 changed files with 3 additions and 0 deletions
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java/src/org/broadinstitute/sting/secondarybase/BasecallingReadModel.java
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@ -232,6 +232,9 @@ public class BasecallingReadModel {
int actualBasePrevIndex = (correctForContext && cycle > 0) ? BaseUtils.simpleBaseToBaseIndex(basePrev) : 0;
int actualBaseCurIndex = BaseUtils.simpleBaseToBaseIndex(baseCur);
if (actualBasePrevIndex == -1) { actualBasePrevIndex = BaseUtils.getRandomBaseIndex(); }
if (actualBaseCurIndex == -1) { actualBaseCurIndex = BaseUtils.getRandomBaseIndex(); }
double residualTheories = (double) (dist.length*dist[0].length - 1);
for (int basePrevIndex = 0; basePrevIndex < dist.length; basePrevIndex++) {