#!/bin/bash

inputFile=$1
outputFile=$2
outputDir=$3
min_freq=$4
min_cells=$5

dir="$(cd "$(dirname "$0")" && pwd)"
mkdir $outputDir


Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputFile $min_freq $min_cells 2>&1
cp $dir/jquery-1.11.0.min.js $outputDir
cp $dir/script.js $outputDir
cp $dir/style.css $outputDir
cp $dir/tabber.js $outputDir

echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)</center></html>" > $outputFile

cd $outputDir

header="<html><head><script type='text/javascript' src='jquery-1.11.0.min.js'></script><script type='text/javascript' src='tabber.js'></script><script type='text/javascript' src='script.js'></script><link rel='stylesheet' type='text/css' href='style.css'></head><div id='hidden_div' style='display: none;'></div>"
singles=()
pairs_BM_PB=()
pairs_Left_Right=()
pairs_R_Dx=()
while read patient sample1 sample2 type
do
	echo "$patient"
	html="${patient}.html"
	echo "$header" > $html
	if [[ "$type" == *pair* ]] ; then
		if [[ "$sample1" == *_BM* ]] || [[ "$sample1" == *_PB* ]] ; then
			pairs_BM_PB+=( "$patient" )
		elif [[ "$sample1" == *_Left* ]] || [[ "$sample1" == *_Right* ]] ; then
			pairs_Left_Right+=( "$patient" )
		else
			pairs_R_Dx+=( "$patient" )
		fi
	else
		singles+=( "$patient" )
	fi
	oldLocus=""
	sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
	sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
	tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
	echo "<div class='tabber'>" >> $html
	echo "<div class='tabbertab' title='Data frequency'>" >> $html
	echo "<table><tr><td style='vertical-align:top;'>" >> $html
	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> $html
	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> $html
	echo "<tbody>" >> $html
	while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
	do
		if [ "$locus" != "$oldLocus" ] ; then
			echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> $html
			echo "<tr><td><b>$locus</b></td>" >> $html
		else
			echo "<td></td>" >> $html
		fi
		echo "<td>$v_segment</td>" >> $html
		echo "<td>$j_segment</td>" >> $html
		echo "<td>>$cut_off_value</td>" >> $html 
		if [ "$both" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$both</td>" >> $html
		else
			echo "<td>$both</td>" >> $html
		fi
		if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> $html
		else
			echo "<td>$one</td>" >> $html
		fi
		echo "<td>$read_count1</td>" >> $html
		if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> $html
		else
			echo "<td>$two</td>" >> $html
		fi
		echo "<td>$read_count2</td>" >> $html
		echo "<td>$sum</td>" >> $html
		echo "<td>${percent}&#37;</td>" >> $html
		echo "</tr>" >> $html
		oldLocus="$locus"	
	done < tmp.txt
	echo "</tbody></table>" >> $html
	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> $html
	echo "</div>" >> $html
	echo "<div class='tabbertab' title='Graphs frequency'>" >> $html
	echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> $html
	echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> $html
	echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> $html
	
	tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
	echo "<div class='tabbertab' title='Data reads'>" >> $html
	echo "<table><tr><td style='vertical-align:top;'>" >> $html
	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> $html
	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> $html
	echo "<tbody>" >> $html
	while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
	do
		if [ "$locus" != "$oldLocus" ] ; then
			echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> $html
			echo "<tr><td><b>$locus</b></td>" >> $html
		else
			echo "<td></td>" >> $html
		fi
		echo "<td>$v_segment</td>" >> $html
		echo "<td>$j_segment</td>" >> $html
		echo "<td>>$cut_off_value</td>" >> $html 
		if [ "$both" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$both</td>" >> $html
		else
			echo "<td>$both</td>" >> $html
		fi
		if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> $html
		else
			echo "<td>$one</td>" >> $html
		fi
		echo "<td>$read_count1</td>" >> $html
		if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> $html
		else
			echo "<td>$two</td>" >> $html
		fi
		echo "<td>$read_count2</td>" >> $html
		echo "<td>$sum</td>" >> $html
		echo "<td>${percent}&#37;</td>" >> $html
		echo "</tr>" >> $html
		oldLocus="$locus"
	done < tmp.txt
	echo "</tbody></table>" >> $html
	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> $html
	echo "</div>" >> $html
	echo "<div class='tabbertab' title='Graphs reads'>" >> $html
	echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
	echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> $html
	echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> $html
	echo "</div>" >> $html
	echo "</div>" >> $html
	echo "</html>" >> $html
done < patients.txt

html="index.html"
echo "<html>" > $html
echo "<table>" >> $html
echo "<tr><td><b>Singles:</b></td></tr>" >> $html
for patient in "${singles[@]}"
do
	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
done
echo "<tr><td><b>Pairs (Left & Right):</b></td></tr>" >> $html
for patient in "${pairs_Left_Right[@]}"
do
	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
done
echo "<tr><td><b>Pairs (BM & PB):</b></td></tr>" >> $html
for patient in "${pairs_BM_PB[@]}"
do
	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
done
echo "<tr><td><b>Pairs (Dx & R):</b></td></tr>" >> $html
for patient in "${pairs_R_Dx[@]}"
do
	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
done
echo "<tr><td><b>Triplets:</b></td></tr>" >> $html

while read sample1 sample2 sample3
do
	sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
	sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
	sample3="$(echo ${sample3} | tr -d '\r' | tr -d '\n')"
	patient="${sample1}_${sample2}_${sample3}"
	echo "$patient"
	html="${patient}.html"
	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "index.html"
	echo "$header" > $html
	oldLocus=""
	tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
	echo "<div class='tabber'>" >> $html
	echo "<div class='tabbertab' title='Data frequency'>" >> $html
	echo "<table><tr><td style='vertical-align:top;'>" >> $html
	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> $html
	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_All</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Number of sequences_$sample3</th><th>Read Count $sample3</th></thead>" >> $html
	echo "<tbody>" >> $html
	while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3
	do
		if [ "$locus" != "$oldLocus" ] ; then
			echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> $html
			echo "<tr><td><b>$locus</b></td>" >> $html
		else
			echo "<td></td>" >> $html
		fi
		echo "<td>$v_segment</td>" >> $html
		echo "<td>$j_segment</td>" >> $html
		echo "<td>>$cut_off_value</td>" >> $html 
		if [ "$all" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$all</td>" >> $html
		else
			echo "<td>$all</td>" >> $html
		fi
		if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> $html
		else
			echo "<td>$one</td>" >> $html
		fi
		echo "<td>$read_count1</td>" >> $html
		if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> $html
		else
			echo "<td>$two</td>" >> $html
		fi
		echo "<td>$read_count2</td>" >> $html
		if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$three</td>" >> $html
		else
			echo "<td>$three</td>" >> $html
		fi
		echo "<td>$read_count3</td>" >> $html
		echo "</tr>" >> $html
		oldLocus="$locus"	
	done < tmp.txt
	echo "</tbody></table>" >> $html
	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> $html
	echo "</div>" >> $html
	echo "<div class='tabbertab' title='Graphs frequency'>" >> $html
	echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
	echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_all.png' width='1280' height='720' /></a><br />" >> $html
	
	tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
	echo "<div class='tabbertab' title='Data reads'>" >> $html
	echo "<table><tr><td style='vertical-align:top;'>" >> $html
	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> $html
	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_All</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Number of sequences_$sample3</th><th>Read Count $sample3</th></thead>" >> $html
	echo "<tbody>" >> $html
	while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3 
	do
		if [ "$locus" != "$oldLocus" ] ; then
			echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> $html
			echo "<tr><td><b>$locus</b></td>" >> $html
		else
			echo "<td></td>" >> $html
		fi
		echo "<td>$v_segment</td>" >> $html
		echo "<td>$j_segment</td>" >> $html
		echo "<td>>$cut_off_value</td>" >> $html 
		if [ "$all" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$all</td>" >> $html
		else
			echo "<td>$all</td>" >> $html
		fi
		if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> $html
		else
			echo "<td>$one</td>" >> $html
		fi
		echo "<td>$read_count1</td>" >> $html
		if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> $html
		else
			echo "<td>$two</td>" >> $html
		fi
		echo "<td>$read_count2</td>" >> $html
		if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$three</td>" >> $html
		else
			echo "<td>$three</td>" >> $html
		fi
		echo "<td>$read_count3</td>" >> $html
		echo "</tr>" >> $html
		oldLocus="$locus"
	done < tmp.txt
	echo "</tbody></table>" >> $html
	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> $html
	echo "</div>" >> $html
	echo "<div class='tabbertab' title='Graphs reads'>" >> $html
	echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
	echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_all.png' width='1280' height='720' /></a><br />" >> $html
	echo "</div>" >> $html
	echo "</div>" >> $html
	echo "</html>" >> $html
done < triplets.txt
rm tmp.txt


html="index.html"

echo "</table>" >> $html
echo "</html>" >> $html

