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Added an epsilon (1e-4) to the tertiary and quaternary base hypotheses. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@488 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-22 00:01:37 +00:00
parent 2ac240d78b
commit 5b8502745a
1 changed files with 9 additions and 1 deletions
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10
java/src/org/broadinstitute/sting/utils/BasicPileup.java
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@ -156,8 +156,16 @@ abstract public class BasicPileup implements Pileup {
byte[] sqs = (byte[]) read.getAttribute("SQ");
if (sqs != null && QualityUtils.compressedQualityToBaseIndex(sqs[offset]) != bestBaseIndex) {
double epsilon = 1e-4;
int secondBestBaseIndex = QualityUtils.compressedQualityToBaseIndex(sqs[offset]);
dist[readIndex][secondBestBaseIndex] = (1.0 - dist[readIndex][bestBaseIndex]);
dist[readIndex][secondBestBaseIndex] = (1.0 - dist[readIndex][bestBaseIndex] - 2.0*epsilon);
for (int baseIndex = 0; baseIndex < 4; baseIndex++) {
if (baseIndex != bestBaseIndex && baseIndex != secondBestBaseIndex) {
dist[readIndex][baseIndex] = epsilon;
}
}
} else {
for (int baseIndex = 0; baseIndex < 4; baseIndex++) {
if (baseIndex != bestBaseIndex) {