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Corrected the use of the prior. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@284 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-03 15:47:47 +00:00
parent b854c24575
commit 15151ac125
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/playground/fourbasecaller/BasecallingBaseModel.java
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@ -94,6 +94,8 @@ public class BasecallingBaseModel {
} }
double[][] probdist = new double[4][4]; double[][] probdist = new double[4][4];
double probPrev = (cycle == 0) ? 1.0 : QualityUtils.qualToProb(qualPrev);
int baseIndex = (cycle == 0) ? 0 : baseToBaseIndex(basePrev);
for (int basePrevIndex = 0; basePrevIndex < ((cycle == 0) ? 1 : 4); basePrevIndex++) { for (int basePrevIndex = 0; basePrevIndex < ((cycle == 0) ? 1 : 4); basePrevIndex++) {
for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) { for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) {
@ -106,7 +108,7 @@ public class BasecallingBaseModel {
DoubleMatrix1D Ax = alg.mult(inverseCovariances[basePrevIndex][baseCurIndex], sub); DoubleMatrix1D Ax = alg.mult(inverseCovariances[basePrevIndex][baseCurIndex], sub);
double exparg = -0.5*alg.mult(sub, Ax); double exparg = -0.5*alg.mult(sub, Ax);
probdist[basePrevIndex][baseCurIndex] = norms[basePrevIndex][baseCurIndex]*Math.exp(exparg); probdist[basePrevIndex][baseCurIndex] = (baseIndex == basePrevIndex ? probPrev : 1.0 - probPrev)*norms[basePrevIndex][baseCurIndex]*Math.exp(exparg);
} }
} }