#!/usr/bin/env sh

#assembly one paired fa with hisat2+stringtie

READ1=$1
READ2=$2
GENOME=$3
OUTPATH=$4

SamName="hisat_out.sam"

if [ $# -ne 4 ]
then
    echo "Usage: assembly.sh read1.fa read2.fa genome outpath"
    exit 1
fi

if [ ! -d $OUTPATH ]
then
    echo $OUTPATH
    mkdir $OUTPATH
fi
#hisat
BamName=$OUTPATH"/hisat_out_sorted.bam"
hisatOrder=" hisat2 --fr -f -p 8 -1 "$READ1" -2 "$READ2" -x"$GENOME" -S"$OUTPATH"/"$SamName
samSortOrder=" samtools sort "$OUTPATH"/"$SamName" > "$BamName
GtfName=$OUTPATH"/hisat_out.gtf"
stringtieOrder=" stringtie "$BamName" -o "$GtfName" -p 8"
eval $hisatOrder
eval $samSortOrder && rm $OUTPATH"/"$SamName
eval $stringtieOrder