From eaf6279d48d77b149fcf8ac4e8e8429c9aea9559 Mon Sep 17 00:00:00 2001
From: Ami Levy-Moonshine <ami@broadinstitute.org>
Date: Fri, 25 Jan 2013 11:47:30 -0500
Subject: [PATCH] adding RBP to the general calling pipeline and few other
 small changes to it (to make it run with the current bundel file names

---
 .../variant/variantcontext/VariantContextUtils.java              | 1 +
 1 file changed, 1 insertion(+)

diff --git a/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
index b07040748..0a848fba1 100644
--- a/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
@@ -878,6 +878,7 @@ public class VariantContextUtils {
     }
 
     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() ) {
             String name = mergedSampleName(oneVC.getSource(), g.getSampleName(), uniqifySamples);
             if ( ! mergedGenotypes.containsSample(name) ) {