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Bases 'A' and 'a' (etc.) no longer considered different. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3339 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-05-10 14:53:38 +00:00
parent ec543b7b62
commit 4a7902bb8e
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java
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@ -119,7 +119,7 @@ public class ComputeConfusionMatrix extends LocusWalker<Integer, Integer> {
} }
private void incrementConfusionCounts(String context, String altBase, String refBase) { private void incrementConfusionCounts(String context, String altBase, String refBase) {
String key = String.format("%s:%s:%s", context, altBase, refBase); String key = String.format("%s:%s:%s", context, altBase.toUpperCase(), refBase.toUpperCase());
Integer counts = confusionCounts.get(key); Integer counts = confusionCounts.get(key);
if (counts == null) { counts = 0; } if (counts == null) { counts = 0; }