#!/bin/bash

checkExitCode() {
if [ $? -ne 0 ]; then
	echo "Error"
	exit 1;
fi
}

BASEDIR=`dirname $0`

if [ $# -lt 1 ]; then echo "Error No inputs provided" && exit 1; fi

. $BASEDIR/io.sh 2 2 5 "$@"

echo $OUTPUTS1
# Append the location of bowtie2 software to the path - required for TOPHAT2
export PATH=$PATH:$BOWTIE2_HOME/
checkExitCode

# Take a zipped input file containing a collection of FASTQ files and get a space-sep list -> very hacky.
# Accomodating only paired end FASTQ reads
SSV_INPUTS1=`/usr/bin/unzip -Z1 $INPUTS1 | tr "\n" " "`
echo $SSV_INPUTS1

# Extracting the file-collection from zipped input file
/usr/bin/unzip $INPUTS1 -d $PWD
checkExitCode

# Get the bowtie2 reference indices for the input fasta files (currently hg19 and hs37d5 only) -sort of hacky
# Formatting path/prefix to the location of the input fasta file (for example: <path>/hg19.fa => refix: <path>/hg19)
# Note: FASTA file extension needs to be <input>.fa (not <input>.fasta) 
# All bowtie indices should be in the same directory as <input>.fa and have the prefix - <input>.*.bt2
BOWTIE2_REFIX=`echo $INPUTS2 | cut -f 1 -d '.'`

INPUT1_BASE=`basename $INPUTS1`
INPUT_NOEXT=`echo $INPUT1_BASE | cut -f 1 -d '.'`
echo $INPUT_NOEXT

#TOPHATOUTDIR=$PWD/tophat_out
TOPHATOUTDIR=$PWD/$INPUT_NOEXT
echo $TOPHATOUTDIR
checkExitCode

echo $TOPHAT2_HOME/tophat2 -o $INPUT_NOEXT --no-coverage-search --keep-tmp --segment-length $PARAMS1 --max-multihits $PARAMS2 $BOWTIE2_REFIX $SSV_INPUTS1 
$TOPHAT2_HOME/tophat2 -o $INPUT_NOEXT --no-coverage-search --keep-tmp --segment-length $PARAMS1 --max-multihits $PARAMS2 $BOWTIE2_REFIX $SSV_INPUTS1 
checkExitCode

# Rename outputs
echo mv $TOPHATOUTDIR/accepted_hits.bam $OUTPUTS1
mv $TOPHATOUTDIR/accepted_hits.bam $OUTPUTS1
mv $TOPHATOUTDIR/unmapped.bam $OUTPUTS2
mv $TOPHATOUTDIR/junctions.bed $OUTPUTS3
mv $TOPHATOUTDIR/insertions.bed $OUTPUTS4
mv $TOPHATOUTDIR/deletions.bed $OUTPUTS5
checkExitCode