zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

tell UnifiedGenotyper to return calls at all bases 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1941 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-30 03:10:44 +00:00
parent 4ee1d6f733
commit 4bdb5b03bd
1 changed files with 1 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
View File

@ -64,6 +64,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
UnifiedArgumentCollection uac = new UnifiedArgumentCollection(); UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
ug.initialize(); ug.initialize();
uac.baseModel = BaseMismatchModel.THREE_STATE; uac.baseModel = BaseMismatchModel.THREE_STATE;
uac.ALL_BASES = true;
ug.setUnifiedArgumentCollection(uac); ug.setUnifiedArgumentCollection(uac);
// refWindow = new ReferenceContextWindow(nPreviousBases); // refWindow = new ReferenceContextWindow(nPreviousBases);
usePreviousBases = new ArrayList<Boolean>(); usePreviousBases = new ArrayList<Boolean>();