Commit a9873805 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

enable multiple read inputs

parent 8dfacc66
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+16 −16
Original line number Diff line number Diff line
@@ -145,8 +145,8 @@ for op in "$@";do
                while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]]
                    do
                    echo "file: $arg"
                    read1+="${1/%\//}_R1_001"
                    read2+="${1/%\//}_R2_001"
                    read1+=("${1/%\//}_R1_001")
                    read2+=("${1/%\//}_R2_001")
                    shift
                    arg=$1
                done
@@ -178,13 +178,13 @@ for op in "$@";do
            shift
            if [[ "$1" != "" ]]
                then
                while [[ "$1" != "-"* ]]
                arg=$1
                while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]]
                    do
                    if [[ "$1" != "" ]]
                        then
                    echo "file: $arg"
                    read1+=("${1/%\//}")
                    shift
                     fi
                    arg=$1
                done
                skip=true
            else
@@ -198,13 +198,13 @@ for op in "$@";do
            shift
            if [[ "$1" != "" ]]
                then
                while [[ "$1" != "-"* ]]
                arg=$1
                while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]]
                    do
                    if [[ "$1" != "" ]]
                        then
                    echo "file: $arg"
                    read2+=("${1/%\//}")
                    shift
                    fi
                    arg=$1
                done
                skip=true
            else