#!/bin/bash

##anchor sample

echo
while [ -n "$1" ]
do
    case "$1" in
        -h) help="$1"
            shift;;
        -p) thread="$2"
            thread1="-p "
	    thread1+=$thread
	    shift;;
        -f) filetype="-f";; 
        -i) input="$2"
            input1="-i "
	    input1+=$input
	    shift;;
	-l) left="$2"
            left1="-l "
	    left1+=$left
            shift;;
	-r) right="$2"
            right1="-r " 
	    right1+=$right
            shift;;
	-b) bowtieIndex="$2"
	    bowtieIndex1="-b "
	    bowtieIndex1+=$bowtieIndex
            shift;
    esac
    shift
done

if test $help
then
    echo "python input command: AASRA.py $help"
    AASRA.py $help
else
    echo "python input command: AASRA.py $input1 $left1 $right1 $bowtieIndex1"
    AASRA.py $input1 $left1 $right1 $bowtieIndex1

##bowtie2 alignment
    echo "bowtie2 input command: bowtie2 --norc -N 1 -L 16 -i S,0,0.2 $filetype $thread1 -x $bowtieIndex -U anchored_$input -S anchored_$input.sam"
    bowtie2 --norc -N 1 -L 16 -i S,0,0.2 $filetype $thread1 -x $bowtieIndex -U anchored_$input -S anchored_$input.sam
fi