From 38452d8964d484201488be249ca405de9350da4e Mon Sep 17 00:00:00 2001
From: hrehrauer <Hubert.Rehrauer@fgcz.uzh.ch>
Date: Thu, 29 Oct 2015 08:47:27 +0100
Subject: [PATCH] fix featureCounts

---
 R/app-featureCounts.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/app-featureCounts.R b/R/app-featureCounts.R
index c82010c6d..f209a4868 100644
--- a/R/app-featureCounts.R
+++ b/R/app-featureCounts.R
@@ -33,7 +33,7 @@ ezMethodFeatureCounts = function(input=NULL, output=NULL, param=NULL){
                               strandSpecific=switch(param$strandMode, "both"=0, "sense"=1, "antisense"=2, stop("unsupported strand mode: ", param$strandMode)),
                               minMQS=param$minMapQuality,
                               readExtension5=0,readExtension3=0,read2pos=NULL,
-                              minReadOverlap=param$minFeatureOverlap,
+                              minOverlap=param$minFeatureOverlap,
                               countSplitAlignmentsOnly=FALSE,
                               countMultiMappingReads=param$keepMultiHits,
                               countPrimaryAlignmentsOnly=param$countPrimaryAlignmentsOnly,