#!/usr/bin/env sh

#assembly one single end unstrand fastq with hisat2+stringtie
READ1=$1
GENOME=$2
OUTPATH=$3
SamName="hisat_out.sam"

if [ $# -ne 3 ]
then
    echo "Usage: assembly.sh read1.fastq genome outpath"
    exit 1
fi

if [ ! -d $OUTPATH ]
then
    echo $OUTPATH
    mkdir $OUTPATH
fi
#hisat
BamName=$OUTPATH"/hisat_out_sorted.bam"
hisatOrder=" hisat2 -p 8 -U "$READ1" -x "$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 $hisatOrder
eval $samSortOrder && rm $OUTPATH"/"$SamName
eval $stringtieOrder