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

Fix for variant summary -- now treats all 50 bp deletions or insertions as CNVs

This commit is contained in:
Mark DePristo 2011-12-07 09:02:49 -05:00
parent 3060a4a15e
commit 6bf18899df
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
View File

@ -184,7 +184,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
return Type.SNP; return Type.SNP;
case INDEL: case INDEL:
for ( int l : vc.getIndelLengths() ) for ( int l : vc.getIndelLengths() )
if ( l > MAX_INDEL_LENGTH ) if ( Math.abs(l) > MAX_INDEL_LENGTH )
return Type.CNV; return Type.CNV;
return Type.INDEL; return Type.INDEL;
case SYMBOLIC: case SYMBOLIC: