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bug fixed when reference name was passed as a string instead of actual reference bases 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@416 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-04-14 21:46:27 +00:00
parent 222c4e5865
commit 9d56355abe
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
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@ -25,7 +25,7 @@ public class AlignmentUtils {
* @return * @return
*/ */
public static int numMismatches(SAMRecord r, ReferenceSequence ref) { public static int numMismatches(SAMRecord r, ReferenceSequence ref) {
return numMismatches(r, ref.getBases().toString()); return numMismatches(r, new String(ref.getBases()));
} }
public static int numMismatches(SAMRecord r, String ref) { public static int numMismatches(SAMRecord r, String ref) {