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Fix bug wherein aligner could be closed prior to its being used to lowercase sequences.

This commit is contained in:
Christopher Hartl 2011-07-21 13:21:48 -04:00
parent 7054c5342f
commit 2f5d10d16b
1 changed files with 1 additions and 3 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
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@ -228,14 +228,12 @@ public class ValidationAmplicons extends RodWalker<Integer,Integer> {
} }
public void onTraversalDone(Integer fin ) { public void onTraversalDone(Integer fin ) {
if(aligner != null)
aligner.close();
validateSequence(); validateSequence();
if ( doNotUseBWA ) { if ( doNotUseBWA ) {
lowerRepeats(); lowerRepeats();
} else { } else {
lowerNonUniqueSegments(); lowerNonUniqueSegments();
aligner.close();
} }
print(); print();
} }