correct paths to restore cloupe

### 1.0.1

- improved set up call to handle restoring cloupe files for 10x

- support for index files for testing 10x

- checking for dual index files for inDrops-v3, SmartSeq3 and Sci-Seq

- adds whitelists for SmartSeq3 and MARS-Seq-2.0

### 1.0.0

- full documentation of all features

install=false

######convert version#####

convertversion="1.0.0.9004"

convertversion="1.0.1.9000"

##########

        sed -i '/output_for_cloupe/s/^#*#//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro 

        ## remove calling CLOUPE_PREPROCESS

        ### iterate over all files calling CLOUPE_PREPROCESS

        for file in $(grep -l  "call CLOUPE_PREPROCESS"  ${cellrangerpath}cs/${cellrangerversion}/mro/*.mro )

        for file in $(grep -l  "call CLOUPE_PREPROCESS"  ${cellrangerpath}-cs/${cellrangerversion}/mro/*.mro )

        do

            #find  start of CLOUPE_PREPROCESS call

            num=$(grep -n "call CLOUPE_PREPROCESS" $file |  head -n 1 | cut -d":" -f1)