Loading launch_universc.sh +16 −15 Original line number Diff line number Diff line Loading @@ -853,6 +853,7 @@ if [[ $verbose ]]; then echo " checking option: --index1 and --index2" fi #index 1 if [[ $setup == "false" ]]; then if [[ ${#index1[@]} -ne ${#read1[@]} ]]; then Loading @@ -861,7 +862,7 @@ if [[ $setup == "false" ]]; then echo " either give no index1 file, or give index1 file for each and every read1 file" exit 1 else if [[ $verbose ]] then if [[ $verbose ]]; then echo " No index files given. Automatically detecing from R1 and R2 file names..." fi r1_list=("${read1[@]}") Loading Loading @@ -898,16 +899,16 @@ if [[ $setup == "false" ]]; then i1_list[$j]=$i1_read fi done read1=("$r1_{list[@]}") read2=("$r2_{list[@]}") if [ ${#i1_list[@]} -eq 0 ]; then read1=("${r1_list[@]}") read2=("${r2_list[@]}") if [[ ${#i1_list[@]} -eq 0 ]]; then if [[ $verbose ]]; then echo "No index files found" fi else if [ ${#i1_list[@]} -eq 0 ]; then index1=("${i1_list[@]}") if [[ $verbose ]]; then echo "echo " index files found ${#index1[@]} I1s: ${index1[@]}" echo " index files found ${#index1[@]} I1s: ${index1[@]}" fi fi fi Loading @@ -924,7 +925,7 @@ if [[ $setup == "false" ]]; then echo " for $technology, either give no index files or give index1 and index2 for each and every read1 and read2 file" exit 1 else if [[ $verbose ]] then if [[ $verbose ]]; then echo " No index files given. Automatically detecing from R1 and R2 file names..." fi r1_list=("${read1[@]}") Loading @@ -951,14 +952,14 @@ if [[ $setup == "false" ]]; then i2_list[$j]=$i2_read fi done if [ ${#i2_list[@]} -eq 0 ]; then if [[ ${#i2_list[@]} -eq 0 ]]; then if [[ $verbose ]]; then echo "Dual index files not found" fi else if [ ${#i2_list[@]} -eq 0 ]; then index2=("${i2_list[@]}") if [[ $verbose ]]; then echo "echo " index files found ${#index2[@]} I2s: ${index2[@]}" echo " index files found ${#index2[@]} I2s: ${index2[@]}" fi fi fi Loading @@ -970,7 +971,7 @@ if [[ $setup == "false" ]]; then fi fi exit 0 if [[ $verbose ]]; then echo " ${#read1[@]} read1s: ${read1[@]}" Loading Loading
launch_universc.sh +16 −15 Original line number Diff line number Diff line Loading @@ -853,6 +853,7 @@ if [[ $verbose ]]; then echo " checking option: --index1 and --index2" fi #index 1 if [[ $setup == "false" ]]; then if [[ ${#index1[@]} -ne ${#read1[@]} ]]; then Loading @@ -861,7 +862,7 @@ if [[ $setup == "false" ]]; then echo " either give no index1 file, or give index1 file for each and every read1 file" exit 1 else if [[ $verbose ]] then if [[ $verbose ]]; then echo " No index files given. Automatically detecing from R1 and R2 file names..." fi r1_list=("${read1[@]}") Loading Loading @@ -898,16 +899,16 @@ if [[ $setup == "false" ]]; then i1_list[$j]=$i1_read fi done read1=("$r1_{list[@]}") read2=("$r2_{list[@]}") if [ ${#i1_list[@]} -eq 0 ]; then read1=("${r1_list[@]}") read2=("${r2_list[@]}") if [[ ${#i1_list[@]} -eq 0 ]]; then if [[ $verbose ]]; then echo "No index files found" fi else if [ ${#i1_list[@]} -eq 0 ]; then index1=("${i1_list[@]}") if [[ $verbose ]]; then echo "echo " index files found ${#index1[@]} I1s: ${index1[@]}" echo " index files found ${#index1[@]} I1s: ${index1[@]}" fi fi fi Loading @@ -924,7 +925,7 @@ if [[ $setup == "false" ]]; then echo " for $technology, either give no index files or give index1 and index2 for each and every read1 and read2 file" exit 1 else if [[ $verbose ]] then if [[ $verbose ]]; then echo " No index files given. Automatically detecing from R1 and R2 file names..." fi r1_list=("${read1[@]}") Loading @@ -951,14 +952,14 @@ if [[ $setup == "false" ]]; then i2_list[$j]=$i2_read fi done if [ ${#i2_list[@]} -eq 0 ]; then if [[ ${#i2_list[@]} -eq 0 ]]; then if [[ $verbose ]]; then echo "Dual index files not found" fi else if [ ${#i2_list[@]} -eq 0 ]; then index2=("${i2_list[@]}") if [[ $verbose ]]; then echo "echo " index files found ${#index2[@]} I2s: ${index2[@]}" echo " index files found ${#index2[@]} I2s: ${index2[@]}" fi fi fi Loading @@ -970,7 +971,7 @@ if [[ $setup == "false" ]]; then fi fi exit 0 if [[ $verbose ]]; then echo " ${#read1[@]} read1s: ${read1[@]}" Loading
