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Reverse qualities when read seq. is reverse complemented 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1417 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2009-08-12 20:17:35 +00:00
parent 144b424933
commit ba2a3d8a58
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/BamToFastqWalker.java
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@ -23,7 +23,7 @@ public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
} else { } else {
out.println(BaseUtils.simpleReverseComplement(read.getReadString())); out.println(BaseUtils.simpleReverseComplement(read.getReadString()));
out.println("+"); out.println("+");
out.println(BaseUtils.simpleReverseComplement(read.getBaseQualityString())); out.println(BaseUtils.reverse(read.getBaseQualityString()));
} }
return 1; return 1;