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Fixed an issue with VCF combine in sites like the following: 

Broad: Filtered     BC: No call

These were being treated the same as

Broad: Call         BC: No call

Added some verbosity to separate them.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3686 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-06-30 16:49:31 +00:00
parent 66931d433c
commit 52a474b27d
1 changed files with 2 additions and 0 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/vcf/VCFCombine.java
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@ -204,6 +204,8 @@ public class VCFCombine extends RodWalker<VCFRecord, VCFWriter> {
set = priority2 + "-filteredInOther"; set = priority2 + "-filteredInOther";
call = vcf2; call = vcf2;
} }
} else {
set = priority1 + "-filteredAndNoCall";
} }
} else { // good call } else { // good call
if ( vcf2 != null ) { if ( vcf2 != null ) {