Loading launch_universc.sh +209 −210 Original line number Diff line number Diff line Loading @@ -980,8 +980,8 @@ if [[ $verbose ]]; then echo "barcode length: $barcodelength" echo "barcode default: $barcode_default" fi barcodeadjust=`echo $(($barcodelength-$barcode_default))` umiadjust=`echo $(($umilength-$umi_default))` barcodeadjust=`echo $((${barcodelength} - ${barcode_default}))` umiadjust=`echo $((${umilength}-${umi_default}))` if [[ $verbose ]]; then echo "barcode adjust: $barcodeadjust " fi Loading Loading @@ -1573,7 +1573,6 @@ if [[ "$technology" == "quartz-seq" ]] || [[ "$technology" == "ramda-seq" ]] || R1_file=${read1[$(( $ii - 1 ))]} R2_file=$(echo $R1_file | perl -pne 's/(.*)_R1/$1_R2/' ) I1_file=$(echo $R1_file | perl -pne 's/(.*)_R1/$1_I1/' ) if [[ $verbose ]]; then echo $R1_file echo $R2_file Loading @@ -1581,7 +1580,7 @@ if [[ "$technology" == "quartz-seq" ]] || [[ "$technology" == "ramda-seq" ]] || fi #copies index 1 to next line (1st to 2nd) and deletes 3rd line (only if index 1 doesn't contain '+' character) cat $R1_file | sed -E "/x/! s/ (.):(.):(.):(.*)$/ \1:\2:\3:\4$\n\4/g" > $I1_file linediff=$(grep -n "^+" $I1_file | head -n 2 | cut -d: -f1 | awk 'NR==1{p=$1;next} END{print $1-p}') linediff=$(grep -n "^+" $I1_file | head -n 2 | cut -d":" -f 1 | awk 'NR==1{p=$1;next} END{print $1-p}') if [[ $linediff -eq 5 ]];then #remove lines if matched only sed "3~5d" > $I1_file Loading Loading
launch_universc.sh +209 −210 Original line number Diff line number Diff line Loading @@ -980,8 +980,8 @@ if [[ $verbose ]]; then echo "barcode length: $barcodelength" echo "barcode default: $barcode_default" fi barcodeadjust=`echo $(($barcodelength-$barcode_default))` umiadjust=`echo $(($umilength-$umi_default))` barcodeadjust=`echo $((${barcodelength} - ${barcode_default}))` umiadjust=`echo $((${umilength}-${umi_default}))` if [[ $verbose ]]; then echo "barcode adjust: $barcodeadjust " fi Loading Loading @@ -1573,7 +1573,6 @@ if [[ "$technology" == "quartz-seq" ]] || [[ "$technology" == "ramda-seq" ]] || R1_file=${read1[$(( $ii - 1 ))]} R2_file=$(echo $R1_file | perl -pne 's/(.*)_R1/$1_R2/' ) I1_file=$(echo $R1_file | perl -pne 's/(.*)_R1/$1_I1/' ) if [[ $verbose ]]; then echo $R1_file echo $R2_file Loading @@ -1581,7 +1580,7 @@ if [[ "$technology" == "quartz-seq" ]] || [[ "$technology" == "ramda-seq" ]] || fi #copies index 1 to next line (1st to 2nd) and deletes 3rd line (only if index 1 doesn't contain '+' character) cat $R1_file | sed -E "/x/! s/ (.):(.):(.):(.*)$/ \1:\2:\3:\4$\n\4/g" > $I1_file linediff=$(grep -n "^+" $I1_file | head -n 2 | cut -d: -f1 | awk 'NR==1{p=$1;next} END{print $1-p}') linediff=$(grep -n "^+" $I1_file | head -n 2 | cut -d":" -f 1 | awk 'NR==1{p=$1;next} END{print $1-p}') if [[ $linediff -eq 5 ]];then #remove lines if matched only sed "3~5d" > $I1_file Loading
