#!/bin/bash

source $HOME/.bashrc
module load biotools

echo "CIPRES_THREADSPP=$CIPRES_THREADSPP"
echo "CIPRES_NP=$CIPRES_NP"
echo "running: blastn $*"

# 1 gigabyte 
# (( maxsize = (1024 * 1024 * 1024) ))

# Maxsize should be 1 so that we never return blast_output.txt but I changed
# it temporarily to 20meg so that Jim can get and check blast_output.txt for debugging
# maxsize=1
maxsize=20971520

blastn $* && blast_parser.pl blast_output.txt > blast_output_hits.txt
# blast_parser.pl blast_output.txt > blast_output_hits.txt

if [[ -s blast_output_hits.txt ]] ; then
	echo "Parsed blast hits are in blast_output_hits.txt"
	size=$(stat -c %s blast_output.txt)
	if [[ $size -gt $maxsize ]] ; then
		echo "Removing blast alignments, blast_output.txt,  because file size of $size > max allowed size of $maxsize"
		rm blast_output.txt
	fi
fi