X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=erange.git;a=blobdiff_plain;f=docs%2FregionCounts.sh;h=8875513266f785ee537137ec841c790d6d014e04;hp=13c60ad4bb6fd58fed267ff0ffb9772e728bb562;hb=0d3e3112fd04c2e6b44a25cacef1d591658ad181;hpb=5e4ae21098dba3d1edcf11e7279da0d84c3422e4

diff --git a/docs/regionCounts.sh b/docs/regionCounts.sh
index 13c60ad..8875513 100644
--- a/docs/regionCounts.sh
+++ b/docs/regionCounts.sh
@@ -3,7 +3,7 @@ echo 'regionCounts.sh: version 1.0'
 
 cachepages=""
 if [ $# -eq 3 ]; then
-    cachepages="-cache "$3
+    cachepages="--cache "$3
 fi
 
 if [ $# -lt 2 ]; then
@@ -19,7 +19,7 @@ else
 		prefix=`echo $line | cut -f 1 -d ','`
 		rds=`echo $line | cut -f 2 -d ','`
 		if [ -e $rds ]; then
-			python $ERANGEPATH/regionCounts.py $1 $rds $prefix.partcount -force -nomerge -rpkm $cachepages
+			python $ERANGEPATH/regionCounts.py $1 $rds $prefix.partcount --force --nomerge --rpkm $cachepages
 		else
 			echo "could not find $rds - skipping"
 			python $ERANGEPATH/recordLog.py regionCounts.log regionCounts.sh "could not find $rds - skipping"