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

This was busted because it assumed 1 (and only 1) record at each position. However it's possible to have 0 (which generated a NullPointer) or 2+ records (which dropped records). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5361 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-03-02 21:35:50 +00:00
parent 1e68259f5c
commit f0f4bc3363
1 changed files with 1 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -131,8 +131,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation()); Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
if ( ASSUME_IDENTICAL_SAMPLES ) { if ( ASSUME_IDENTICAL_SAMPLES ) {
final VariantContext vc = vcs.iterator().next(); for ( final VariantContext vc : vcs ) {
if( vc != null ) {
vcfWriter.add( vc, ref.getBase() ); vcfWriter.add( vc, ref.getBase() );
} }