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

adding RBP to the general calling pipeline and few other small changes to it (to make it run with the current bundel file names

This commit is contained in:
Ami Levy-Moonshine 2013-01-25 11:47:30 -05:00
parent 0fb7b73107
commit eaf6279d48
1 changed files with 1 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
View File

@ -878,6 +878,7 @@ public class VariantContextUtils {
} }
private static void mergeGenotypes(GenotypesContext mergedGenotypes, VariantContext oneVC, AlleleMapper alleleMapping, boolean uniqifySamples) { private static void mergeGenotypes(GenotypesContext mergedGenotypes, VariantContext oneVC, AlleleMapper alleleMapping, boolean uniqifySamples) {
//TODO: should we add a check for cases when the genotypeMergeOption is REQUIRE_UNIQUE
for ( Genotype g : oneVC.getGenotypes() ) { for ( Genotype g : oneVC.getGenotypes() ) {
String name = mergedSampleName(oneVC.getSource(), g.getSampleName(), uniqifySamples); String name = mergedSampleName(oneVC.getSource(), g.getSampleName(), uniqifySamples);
if ( ! mergedGenotypes.containsSample(name) ) { if ( ! mergedGenotypes.containsSample(name) ) {