#!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
#  THE SOFTWARE.
##########
#
# Sanity check once pipeline is complete to be sure number of lines adds up, deduping
# proceeded appropriately, and that files were created
# Juicer version 1.5

# Start by checking the statistics to see if they add up 
res1=`cat ${splitdir}/*norm*res*`
check1=`cat ${splitdir}/*norm*res* | awk '{s2+=$2; s3+=$3; s4+=$4; s5+=$5; s6+=$6}END{if (s2 != s3+s4+s5+s6){print 0}else{print 1}}'`
if [ $check1 -eq 0 ] || [ -z "$res1" ]
then
    echo "***! Error! The statistics do not add up. Alignment likely failed to complete on one or more files. Run relaunch_prep.sh"
    echo "Stats don't add up.  Check ${outputdir} for results"
    exit 1
fi

# Check the sizes of merged_sort versus the dups/no dups files to be sure
# no reads were lost
total=1
total2=0
total=`ls -l ${outputdir}/merged_sort.txt | awk '{print $5}'`
total2=`ls -l ${outputdir}/merged_nodups.txt ${outputdir}/dups.txt ${outputdir}/opt_dups.txt | awk '{sum = sum + $5}END{print sum}'`

if [ -z $total ] || [ -z $total2 ] || [ $total -ne $total2 ]
then
    echo "***! Error! The sorted file and dups/no dups files do not add up, or were empty. Merge or dedupping likely failed, restart pipeline with -S merge or -S dedup"
    echo "Dups don't add up.  Check ${outputdir} for results"
    exit 1
fi

wctotal=`cat ${splitdir}/*_linecount.txt | awk '{sum+=$1}END{print sum/4}'`
check2=`cat ${splitdir}/*norm*res* | awk '{s2+=$2;}END{print s2}'`
 
if [ $wctotal -ne $check2 ]
then
    echo "***! Error! The number of reads in the fastqs (${wctotal}) is not the same as the number of reads reported in the stats (${check2}), likely due to a failure during alignment"
    echo "Reads don't add up.  Check ${outputdir} for results"
    exit 1
fi

if [ -n "$early" ]
then
    echo "(-: Pipeline successfully completed (-:";
    echo "Run cleanup.sh to remove the splits directory";
    echo "Check ${outputdir} for results"
elif [ -f ${outputdir}/inter.hic ] && [ -s ${outputdir}/inter.hic ] && [ -f ${outputdir}/inter_30.hic ] && [ -s ${outputdir}/inter_30.hic ]
then
    echo "(-: Pipeline successfully completed (-:";
    echo "Run cleanup.sh to remove the splits directory";
    echo "Check ${outputdir} for results"
else
    echo "***! Error! Either inter.hic or inter_30.hic were not created"
    echo "Either inter.hic or inter_30.hic were not created.  Check ${outputdir} for results"
    exit 1
fi