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bin/abyss-bowtie

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# Parse the command line.

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bowtie='bowtie -S'

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while getopts :ij:k:v opt; do

 

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while getopts :j:k:v opt; do

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        case $opt in

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                i) ;;

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                j) bowtie="$bowtie -p$OPTARG";;

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                k) ;;

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                v) ;;

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# Map the reads.

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echo >&2 $bowtie $target "${query[@]}"

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exec abyss-tofastq "${query[@]}" |$bowtie $target -

 

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exec abyss-tofastq -i "${query[@]}" |$bowtie $target -

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