cachepages=""
if [ $# -eq 3 ]; then
- cachepages="-cache "$3
+ cachepages="--cache "$3
fi
if [ $# -lt 2 ]; then
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"