#!/usr/bin/env bash
#this srcipt is to do wheat_bsa
#author lee

#this is fail test, because bash didn't care about the failure of command
#this can prevent the situation that check result of each step, only right can go on
set -Eeuo pipefail

#display for better use and record log of change

Usage(){
    cat <<EOF

Usage:
    $0 Input: Gene ID 
    $0 Haplotype
    $0 Phenotype
    $0 -h (help) (Display this document)

EOF
    exit 1
}

# display help with para -h
[ "$1" = "-h" ] && Usage

#basename:basename---strip directory and suffix from filenames
#dirname:---keep directory only cd `dirname $0` can change the work directory and perform command

### index
OUTPUT_DIR=/public/home/caisl/lee/my_rnaseq/rna
mkdir -p "$OUTPUT_DIR"

LOG_DIR=/public/home/caisl/lee/my_rnaseq/rna
mkdir -p "$LOG_DIR"

ref_seq=/public/home/caisl/lee/my_rnaseq/Triticum_aestivum.IWGSC.dna.toplevel.fa
annotation=/public/home/caisl/lee/my_rnaseq/Triticum_aestivum.IWGSC.51.gtf