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In extended event lines, now prints deletions in verbose format as well (e.g. "-AAT") 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2490 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2009-12-30 21:57:20 +00:00
parent a18e31f5b8
commit 46362ce532
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -91,7 +91,8 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
if ( context.hasExtendedEventPileup() ) {
ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
List<Pair<String,Integer>> eventCounts = indelPileup.getEventStringsWithCounts();
List<Pair<String,Integer>> eventCounts = indelPileup.getEventStringsWithCounts(ref.getBases());
out.printf("%s %s ", indelPileup.getShortPileupString(), rods);
int i = 0;
for ( ; i < eventCounts.size() - 1 ; i++ ) {