correct indexing for multiple files or lanes (8131012b) · Commits · github_fork / Universc

launch_universc.sh

+16 −8

Original line number	Diff line number	Diff line
		@@ -505,8 +505,9 @@ elif [ "$technology" == "icell8" ]; then
		fi

		#auto detect read file format (if one file each)
		for i in ${!read1[@]}
		for j in ${!read1[@]}
		do
		i=$(($j+1))
		read=${read1[$i]}
		echo " checking file format for $read1 ..."
		if [ -f $read ] && [ ! -h $read ]
		@@ -536,8 +537,9 @@ read=${read1[$i]}
		read1[$i]=$read
		done

		for i in ${!read2[@]}
		for j in ${!read2[@]}
		do
		i=$(($j+1))
		read=${read2[$i]}
		echo " checking file format for $read2 ..."
		if [ -f $read ] \|\| [ ! -h $read ]
		@@ -568,8 +570,9 @@ read2[$i]=$read
		done

		echo " checking file name for $read1 ..."
		for i in ${!read1[@]}
		for j in ${!read1[@]}
		do
		i=$(($j+1))
		read=${read1[$i]}
		case $read in
		#check if contains lane before read
		@@ -596,7 +599,7 @@ case $read in
		echo " renaming $read ...";;
		esac
		case $read in
		#check if contains sample before lane
		#check if contains suffix
		(_R1_001.) echo " $read compatible with suffix";;
		(*) echo " converting $read ..."
		#rename file
		@@ -621,8 +624,9 @@ fi
		done

		echo " checking file name for $read2 ..."
		for i in ${!read2[@]}
		for j in ${!read2[@]}
		do
		i=$(($j+1))
		read=${read2[$i]}
		case $read in
		#check if contains lane before read
		@@ -649,13 +653,15 @@ case $read in
		echo " renaming $read ...";;
		esac
		case $read in
		#check if contains sample before lane
		#check if contains suffix
		(_R1_001.) echo " $read compatible with suffix";;
		(*) echo " converting $read ..."
		#rename file
		rename "s/_R1.*\./_R1_001\./" $read
		rename "s/_R1.*\./_R1_001\./" $read
		#update file variable
		read=`echo $read \| sed -e "s/_R1.*\./_R1_001\./g"`
		read=`echo $read \| sed -e "s/_R1.*\./_R1_001\./g"`
		read2[$i]=$read
		echo " renaming $read";;
		esac
		@@ -740,7 +746,8 @@ fi
		mkdir -p $crIN
		if [ -d $crIN ]
		then
		for i in ${!read1[@]}
		for j in ${!read1[@]}
		i=$(($j+1))
		do
		read=${read1[$i]}
		if [ -f $crIN/$read ]
		@@ -755,7 +762,8 @@ if [ -d $crIN ]
		echo "file $crIN/$read kept"
		fi
		done
		for i in ${!read2[@]}
		for j in ${!read2[@]}
		i=$(($j+1))
		do
		read=${read2[$i]}
		if [ -f $crIN/$read ]

Admin message