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change for new char/byte in BaseUtils 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1467 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-08-27 23:47:56 +00:00
parent a639459112
commit 7cf9a54b64
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounter.java
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@ -121,9 +121,9 @@ public class CovariateCounter {
char prevBase = (char)bases[offset - 1]; char prevBase = (char)bases[offset - 1];
if (read.getReadNegativeStrandFlag()) { if (read.getReadNegativeStrandFlag()) {
ref = (char)BaseUtils.simpleComplement(ref); ref = BaseUtils.simpleComplement(ref);
base = (char)BaseUtils.simpleComplement(base); base = BaseUtils.simpleComplement(base);
prevBase = (char)BaseUtils.simpleComplement((char)bases[offset+1]); prevBase = BaseUtils.simpleComplement((char)bases[offset+1]);
cycle = read.getReadLength() - (offset + 1); cycle = read.getReadLength() - (offset + 1);
} }