# HG changeset patch
# User davidvanzessen
# Date 1408354127 14400
# Node ID 8a4183eed741f84f84f26f53b10c6c7c324b4b44
# Parent  d8de51314d3f735623167b6fd820eb582e85e286
Uploaded

diff -r d8de51314d3f -r 8a4183eed741 wrapper.sh
--- a/wrapper.sh	Thu Aug 14 07:17:26 2014 -0400
+++ b/wrapper.sh	Mon Aug 18 05:28:47 2014 -0400
@@ -47,8 +47,15 @@
 		summaryfile="$PWD/summary_${id}.txt"
 		gappedfile="$PWD/gappednt_${id}.txt"
 		filtered="$PWD/filtered_${id}.txt"
-		cat $PWD/$id/*/1_* > $summaryfile
-		cat $PWD/$id/*/2_* > $gappedfile
+		filecount=`ls -l $PWD/$id/ | wc -l`
+		if [ "$filecount" -eq "1" ]
+		then
+			cat $PWD/$id/*/1_* > $summaryfile
+			cat $PWD/$id/*/2_* > $gappedfile
+		else
+			cat $PWD/$id/1_* > $summaryfile
+			cat $PWD/$id/2_* > $gappedfile
+		fi
 		Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered 2>&1
 		
 		final="$PWD/final_${id}.txt"