Loading launch_universc.sh +60 −40 Original line number Diff line number Diff line Loading @@ -890,6 +890,7 @@ if [[ $setup == "false" ]]; then for j in ${!r1_list[@]}; do read=${r1_list[$j]} R1_file=$read if [[ $read == *R1* ]]; then R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' ) R4_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R4/' ) I1_file=$(echo $read | perl -pne 's/(.*)_R1/$1_I1/' ) Loading Loading @@ -917,6 +918,7 @@ if [[ $setup == "false" ]]; then i1_read=$I1_file i1_list[$j]=$i1_read fi fi done read1=("${r1_list[@]}") read2=("${r2_list[@]}") Loading Loading @@ -953,6 +955,7 @@ if [[ $setup == "false" ]]; then for j in ${!r1_list[@]}; do read=${r1_list[$j]} R1_file=$read if [[ $read == *R1* ]]; then R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' ) R3_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R3/' ) I2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_I2/' ) Loading @@ -970,6 +973,7 @@ if [[ $setup == "false" ]]; then i2_read=$I2_file i2_list[$j]=$i2_read fi fi done if [[ ${#i2_list[@]} -eq 0 ]]; then if [[ $verbose ]]; then Loading Loading @@ -1143,6 +1147,22 @@ for key in ${keys[@]}; do fi read=${fullpath} fi if [[ $read == *$readkey* ]]; then if [[ $verbose ]]; then echo " (file) $read contains $readkey" fi else if [[ $verbose ]]; then echo " (file) $read does not contain $readkey" fi readsuffix="${readkey: -1}" rename -f "s/_${readsuffix}\./_R${readsuffix}_001./" $read read=`echo $read | sed -e "s/_${readsuffix}\./_R${readsuffix}_001./g"` if [[ $verbose ]]; then echo " (file) $read contains $readkey" fi fi case $read in #check if contains lane before read *_L0[0123456789][0123456789]_$readkey*) Loading Loading
launch_universc.sh +60 −40 Original line number Diff line number Diff line Loading @@ -890,6 +890,7 @@ if [[ $setup == "false" ]]; then for j in ${!r1_list[@]}; do read=${r1_list[$j]} R1_file=$read if [[ $read == *R1* ]]; then R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' ) R4_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R4/' ) I1_file=$(echo $read | perl -pne 's/(.*)_R1/$1_I1/' ) Loading Loading @@ -917,6 +918,7 @@ if [[ $setup == "false" ]]; then i1_read=$I1_file i1_list[$j]=$i1_read fi fi done read1=("${r1_list[@]}") read2=("${r2_list[@]}") Loading Loading @@ -953,6 +955,7 @@ if [[ $setup == "false" ]]; then for j in ${!r1_list[@]}; do read=${r1_list[$j]} R1_file=$read if [[ $read == *R1* ]]; then R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' ) R3_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R3/' ) I2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_I2/' ) Loading @@ -970,6 +973,7 @@ if [[ $setup == "false" ]]; then i2_read=$I2_file i2_list[$j]=$i2_read fi fi done if [[ ${#i2_list[@]} -eq 0 ]]; then if [[ $verbose ]]; then Loading Loading @@ -1143,6 +1147,22 @@ for key in ${keys[@]}; do fi read=${fullpath} fi if [[ $read == *$readkey* ]]; then if [[ $verbose ]]; then echo " (file) $read contains $readkey" fi else if [[ $verbose ]]; then echo " (file) $read does not contain $readkey" fi readsuffix="${readkey: -1}" rename -f "s/_${readsuffix}\./_R${readsuffix}_001./" $read read=`echo $read | sed -e "s/_${readsuffix}\./_R${readsuffix}_001./g"` if [[ $verbose ]]; then echo " (file) $read contains $readkey" fi fi case $read in #check if contains lane before read *_L0[0123456789][0123456789]_$readkey*) Loading
