enable skipping of conversion (5472487f) · Commits · github_fork / Universc

launch_universc.sh

+12 −7

Original line number	Diff line number	Diff line
		@@ -655,7 +655,7 @@ case $read in
		rename "s/_R1.*\./_R1_001\./" $read
		#update file variable
		read=`echo $read \| sed -e "s/_R1.*\./_R1_001\./g"`
		read1[$i]=$read
		read2[$i]=$read
		echo " renaming $read";;
		esac
		#check if file in directory and link if not
		@@ -825,9 +825,14 @@ for fq in "${read2[@]}"; do
		fi
		done

		if [[ $verbose == "true" ]]
		then
		echo "convert: $convert"
		echo "${crR1s[@]}"
		echo "${crR2s[@]}"
		fi

		if [[ $convert == true ]]
		if [[ $convert == "true" ]]
		then
		if [[ "$technology" == "10x" ]]; then
		echo " 10x files accepted without conversion"
		@@ -837,13 +842,13 @@ if [[ $convert == true ]]
		echo " handling $fq"
		if [[ "$technology" == "nadia" ]]; then
		echo " converting barcodes"
		sed -i '2~4s/^/AAAA/' ${crIN}/$fq #Add AAAA to every read
		echo sed -i '2~4s/^/AAAA/' ${crIN}/$fq #Add AAAA to every read
		echo " converting quality scores"
		sed -i '4~4s/^/IIII/' ${crIN}/$fq #Add quality scores for added bases
		echo sed -i '4~4s/^/IIII/' ${crIN}/$fq #Add quality scores for added bases
		echo " converting UMI"
		sed -i '2~4s/[NATCG][NATCG][NATCG][NATCG][NATCG][NATCG]$/AA/' ${crIN}/$fq #Replace last 6 bases with AA
		echo sed -i '2~4s/[NATCG][NATCG][NATCG][NATCG][NATCG][NATCG]$/AA/' ${crIN}/$fq #Replace last 6 bases with AA
		echo " converting quality scores"
		sed -i '4~4s/......$/II/' ${crIN}/$fq #Replace quality scores for added bases
		echo sed -i '4~4s/......$/II/' ${crIN}/$fq #Replace quality scores for added bases
		elif [[ "$technology" == "icell8" ]]; then
		echo "converting barcodes"
		sed -i '2~4s/^/AAAAA/' ${crIN}/$fq #Add AAAAA to every read

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