#!/usr/bin/env sh

sdir=$(dirname `realpath $0`)
WORKPATH=`realpath $1`

cd ${WORKPATH}
gindex="../input/templateGenome/hs38Chr"
gtf="../input/template.gtf"

makedir(){
    if [ ! -d $1 ]
    then
        mkdir $1
    fi
}

for x in {1..10}
do
    x=`printf "%02d" $x`
    simuout="simu$x"
    makedir $simuout
    file1=sample_${x}_1.fasta
    file2=sample_${x}_2.fasta
    eval "${sdir}/assembly.sh "$file1" "$file2" "$gindex" "$simuout" >>"$simuout"/std.log 2>>"$simuout"/err.log "
done
mkdir ass

stringtie --merge -G $gtf simu01/hisat_out.gtf simu02/hisat_out.gtf simu03/hisat_out.gtf simu04/hisat_out.gtf simu05/hisat_out.gtf simu06/hisat_out.gtf simu07/hisat_out.gtf simu08/hisat_out.gtf simu09/hisat_out.gtf simu10/hisat_out.gtf > ass/merged_with_G.gtf
stringtie --merge simu01/hisat_out.gtf simu02/hisat_out.gtf simu03/hisat_out.gtf simu04/hisat_out.gtf simu05/hisat_out.gtf simu06/hisat_out.gtf simu07/hisat_out.gtf simu08/hisat_out.gtf simu09/hisat_out.gtf simu10/hisat_out.gtf > ass/merged_no_G.gtf