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Ignoring deletions in the primary pileup by default was causing the primary pileup to become shorter than the secondary pileup when building up the secondary base pileup string. This fix makes sure to include the primary Ds within the pileup so that not only are the pileups guaranteed to be the same size, the same offsets will truly correspond with the same read. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2058 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-11-17 17:20:13 +00:00
parent aece7fa4c7
commit 43bd4c8e8f
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/utils/BasicPileup.java
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@ -190,7 +190,7 @@ abstract public class BasicPileup implements Pileup {
if (sbases == null) { return null; }
ArrayList<Byte> pbases = basePileup(reads, offsets);
ArrayList<Byte> pbases = basePileup(reads, offsets,true);
Random generator = new Random();