resolve conflicts and check conversion

#set options

lockfile=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.lock #path for .lock file

lastcallfile=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.last_called #path for .last_called

lastcall=`[ -e $lastcallfile ] && echo 1 || echo ""`

lastcall=`[ -e $lastcallfile ] &&  cat $lastcallfile || echo ""`

barcodedir=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes #folder within cellranger with the whitelist barcodes

barcodefile=""

crIN=input4cellranger #name of the directory with all FASTQ files given to cellranger

    echo " input file format conversion skipped"

fi

echo "barcodes:" $barcodeadjust "umis:" $umiadjust 

#converting barcodes

echo " adjusting barcodes of R1 files"

if [[ $barcodeadjust != 0 ]] && [[ $convert == "true" ]]; then

    if [[ $barcodeadjust -gt 0 ]]; then

        for convFile in "${convFiles[@]}"; do

            echo " handling $convFile ..."

            sed -i "2~2s/^.{${barcodeadjust}}//" $convFile #Trim the first n characters from the beginning of the sequence and quality

            echo "  ${convFile} adjusted"

       done

    elif [[ 0 -gt $barcodeadjust ]]; then

        for convFile in "${convFiles[@]}"; do

            echo " handling $convFile ..."

            toS=`printf '%0.sA' $(seq 1 $(($barcodeadjust * -1)))`

            toQ=`printf '%0.sI' $(seq 1 $(($barcodeadjust * -1)))`

            sed -i "2~4s/^/$toS/" $convFile #Trim the first n characters from the beginning of the sequence

echo " adjusting UMIs of R1 files"

if [[ 0 -gt $umiadjust ]]; then 

    for convFile in "${convFiles[@]}"; do

<<<<<<< HEAD

        echo " handling $convFile ..."

        if [[ "$technology" == "nadia" ]]; then

            echo "  converting barcodes"

            sed -i '2~4s/^/AAAA/' $convFile #Add AAAA to every read

            echo "  converting quality scores"

            sed -i '4~4s/^/IIII/' $convFile #Add quality scores for added bases

            echo "  converting UMI"

            sed -i '2~4s/[NATCG][NATCG][NATCG][NATCG]$//' $convFile #Remove last 4 bases

            echo "  converting quality scores"

            sed -i '4~4s/....$//' $convFile #Replace quality scores for last 4 bases

        elif [[ "$technology" == "icell8" ]]; then

            echo "  converting barcodes"

            sed -i '2~4s/^/AAAAA/' $convFile #Add AAAAA to every read

            echo "  converting quality scores"

            sed -i '4~4s/^/IIIII/' $convFile #Add quality scores for added bases

        fi

=======

        toS=`printf '%0.sA' $(seq 1 $(($umiadjust * -1)))`

        toQ=`printf '%0.sI' $(seq 1 $(($umiadjust * -1)))`

	keeplength=`echo $((${barcode_default}+${umi_default}-($umiadjust * -1)))`

        sed -i "2~4s/$/$toS/" $convFile #Add n characters to the end of the sequence

        sed -i "4~4s/$/$toQ/" $convFile #Add n characters to the end of the quality

        echo "  ${convFile} adjusted"

>>>>>>> 630f098064d4535f192e5fd4ca68bfdc6dd1d966

    done

fi

##########