resolved merge issue (c48bc765) · Commits · github_fork / Universc

launch_universc.sh

+17 −2

Original line number	Diff line number	Diff line
		@@ -346,7 +346,7 @@ if [[ $verbose == "true" ]]; then
		fi

		#check if cellranger is writable
		if [[ ! -w $lockfile ]]; then
		if [[ ! -w $barcodedir ]]; then
		echo "Error: Trying to run cellranger installed at ${cellrangerpath}"
		echo "launch_universc.sh can only run with cellranger installed locally"
		echo "Install cellranger in a directory with write permissions such as /home/`whoami`/local and export to the PATH"
		@@ -354,7 +354,7 @@ if [[ ! -w $lockfile ]]; then
		echo " `whereis cellranger`"
		exit 1
		fi

		exit 0
		#check if technology matches expected inputs
		if [[ "$technology" != "10x" ]] && [[ "$technology" != "nadia" ]] && [[ "$technology" != "icell8" ]]; then
		if [[ "$technology" != "custom"* ]]; then
		@@ -984,6 +984,7 @@ fi
		echo " adjusting UMIs of R1 files"
		if [[ 0 -gt $umiadjust ]]; then
		for convFile in "${convFiles[@]}"; do
		<<<<<<< HEAD
		<<<<<<< HEAD
		toS=`printf '%0.sA' $(seq 1 $(($umiadjust * -1)))`
		toQ=`printf '%0.sI' $(seq 1 $(($umiadjust * -1)))`
		@@ -993,6 +994,8 @@ if [[ 0 -gt $umiadjust ]]; then
		sed -i "4~4s/$/$toQ/" $convFile #Add n characters to the end of the quality
		echo " ${convFile} adjusted"
		=======
		=======
		>>>>>>> 1adfb361a1bc38c600bff617ac8877ca5cc3fdaa
		echo " handling $convFile ..."
		if [[ "$technology" == "nadia" ]]; then
		echo " converting barcodes"
		@@ -1009,7 +1012,19 @@ if [[ 0 -gt $umiadjust ]]; then
		echo " converting quality scores"
		sed -i '4~4s/^/IIIII/' $convFile #Add quality scores for added bases
		fi
		<<<<<<< HEAD
		>>>>>>> e05b998d17d2c79ec3eec9784858acde747671ae
		=======
		=======
		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 "2~2s/^$.\{${keeplength}\}$.*/\1/" $convFile #Trim off everything beyond what is needed
		sed -i "2~4s/$/$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
		>>>>>>> 1adfb361a1bc38c600bff617ac8877ca5cc3fdaa
		done
		fi
		##########

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