0
+ − 1 #!/bin/bash
+ − 2
+ − 3 inputFile=$1
+ − 4 outputFile=$2
+ − 5 outputDir=$3
+ − 6 min_freq=$4
+ − 7 min_cells=$5
+ − 8 merge_on="$6"
+ − 9
+ − 10 dir="$(cd "$(dirname "$0")" && pwd)"
+ − 11 mkdir $outputDir
+ − 12
+ − 13
+ − 14 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputFile $min_freq $min_cells "${merge_on}" 2>&1
+ − 15 cp $dir/jquery-1.11.0.min.js $outputDir
+ − 16 cp $dir/script.js $outputDir
+ − 17 cp $dir/style.css $outputDir
+ − 18 cp $dir/tabber.js $outputDir
+ − 19 mv "$outputFile" "$outputDir/log.html"
+ − 20
+ − 21 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
+ − 22
+ − 23 cd $outputDir
+ − 24
+ − 25 header="<html><head><script type='text/javascript' src='jquery-1.11.0.min.js'></script><script type='text/javascript' src='tabber.js'></script><script type='text/javascript' src='script.js'></script><link rel='stylesheet' type='text/css' href='style.css'></head><div id='hidden_div' style='display: none;'></div>"
+ − 26 singles=()
+ − 27 pairs_BM_PB=()
+ − 28 pairs_Left_Right=()
+ − 29 pairs_R_Dx=()
+ − 30 while read patient sample1 sample2 type
+ − 31 do
+ − 32 echo "$patient"
+ − 33 html="${patient}.html"
+ − 34 echo "$header" > "$html"
+ − 35 if [[ "$type" == *pair* ]] ; then
+ − 36 if [[ "$sample1" == *_BM* ]] || [[ "$sample1" == *_PB* ]] ; then
+ − 37 pairs_BM_PB+=( "$patient" )
+ − 38 elif [[ "$sample1" == *_Left* ]] || [[ "$sample1" == *_Right* ]] ; then
+ − 39 pairs_Left_Right+=( "$patient" )
+ − 40 else
+ − 41 pairs_R_Dx+=( "$patient" )
+ − 42 fi
+ − 43 else
+ − 44 singles+=( "$patient" )
+ − 45 fi
+ − 46 oldLocus=""
+ − 47 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
+ − 48 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
1
+ − 49 tail -n+2 "${patient}_freq.txt" | sed "s/>//" > tmp.txt
0
+ − 50 echo "<div class='tabber'>" >> "$html"
+ − 51 echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
+ − 52 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
+ − 53 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
+ − 54 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"
+ − 55 echo "<tbody>" >> "$html"
+ − 56 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'><table border='0'><tr>"
+ − 57 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
+ − 58 do
+ − 59 if [ "$locus" != "$oldLocus" ] ; then
+ − 60 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html"
+ − 61 echo "<tr><td><b>$locus</b></td>" >> "$html"
+ − 62 else
+ − 63 echo "<td></td>" >> "$html"
+ − 64 fi
+ − 65 echo "<td>$v_segment</td>" >> "$html"
+ − 66 echo "<td>$j_segment</td>" >> "$html"
+ − 67 echo "<td>>$cut_off_value</td>" >> "$html"
+ − 68 if [ "$both" != "0" ] ; then
+ − 69 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$both</td>" >> "$html"
+ − 70 else
+ − 71 echo "<td>$both</td>" >> "$html"
+ − 72 fi
+ − 73 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 74 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> "$html"
+ − 75 else
+ − 76 echo "<td>$one</td>" >> "$html"
+ − 77 fi
+ − 78 echo "<td>$read_count1</td>" >> "$html"
+ − 79 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 80 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> "$html"
+ − 81 else
+ − 82 echo "<td>$two</td>" >> "$html"
+ − 83 fi
+ − 84 echo "<td>$read_count2</td>" >> "$html"
+ − 85 echo "<td>$sum</td>" >> "$html"
+ − 86 echo "<td>${percent}%</td>" >> "$html"
+ − 87 echo "</tr>" >> "$html"
+ − 88 oldLocus="$locus"
+ − 89 if [ "${cut_off_value}" == "0" ] ; then
+ − 90 scatterplot_tab="${scatterplot_tab}<td><img src='${patient}_${sample1}_${sample2}_freq_${locus}_scatter.png' /></td>"
+ − 91 fi
+ − 92 done < tmp.txt
+ − 93 echo "</tbody></table>" >> "$html"
+ − 94 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html"
+ − 95 echo "</div>" >> "$html"
+ − 96 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html"
+ − 97 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> "$html"
+ − 98 echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> "$html"
+ − 99 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html"
+ − 100 echo "${scatterplot_tab}</tr></table></div>" >> "$html"
+ − 101
1
+ − 102 tail -n+2 "${patient}_reads.txt" | sed "s/>//" > tmp.txt
0
+ − 103 echo "<div class='tabbertab' title='Data reads'>" >> "$html"
+ − 104 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
+ − 105 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
+ − 106 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"
+ − 107 echo "<tbody>" >> "$html"
+ − 108 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'><table border='0'><tr>"
+ − 109 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
+ − 110 do
+ − 111 if [ "$locus" != "$oldLocus" ] ; then
+ − 112 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html"
+ − 113 echo "<tr><td><b>$locus</b></td>" >> "$html"
+ − 114 else
+ − 115 echo "<td></td>" >> "$html"
+ − 116 fi
+ − 117 echo "<td>$v_segment</td>" >> "$html"
+ − 118 echo "<td>$j_segment</td>" >> "$html"
+ − 119 echo "<td>>$cut_off_value</td>" >> "$html"
+ − 120 if [ "$both" != "0" ] ; then
+ − 121 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$both</td>" >> "$html"
+ − 122 else
+ − 123 echo "<td>$both</td>" >> "$html"
+ − 124 fi
+ − 125 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 126 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> "$html"
+ − 127 else
+ − 128 echo "<td>$one</td>" >> "$html"
+ − 129 fi
+ − 130 echo "<td>$read_count1</td>" >> "$html"
+ − 131 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 132 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> "$html"
+ − 133 else
+ − 134 echo "<td>$two</td>" >> "$html"
+ − 135 fi
+ − 136 echo "<td>$read_count2</td>" >> "$html"
+ − 137 echo "<td>$sum</td>" >> "$html"
+ − 138 echo "<td>${percent}%</td>" >> "$html"
+ − 139 echo "</tr>" >> "$html"
+ − 140 oldLocus="$locus"
+ − 141 if [ "${cut_off_value}" == "0" ] ; then
+ − 142 scatterplot_tab="${scatterplot_tab}<td><img src='${patient}_${sample1}_${sample2}_reads_${locus}_scatter.png' /></td>"
+ − 143 fi
+ − 144 done < tmp.txt
+ − 145 echo "</tbody></table>" >> "$html"
+ − 146 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html"
+ − 147 echo "</div>" >> "$html"
+ − 148 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html"
+ − 149 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> "$html"
+ − 150 echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> "$html"
+ − 151 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> "$html"
+ − 152 echo "${scatterplot_tab}</tr></table></div>" >> "$html"
+ − 153 echo "</div>" >> "$html"
+ − 154 echo "</div>" >> "$html"
+ − 155 echo "</html>" >> "$html"
+ − 156 done < patients.txt
+ − 157
+ − 158 html="index.html"
+ − 159 echo "<html>" > $html
+ − 160 echo "<table>" >> "$html"
+ − 161 echo "<tr><td><b>Singles (<a href='singles_freq_scatterplot.png'>Frequency scatterplot</a>, <a href='singles_reads_scatterplot.png'>Reads scatterplot</a>):</b></td></tr>" >> "$html"
+ − 162 for patient in "${singles[@]}"
+ − 163 do
+ − 164 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
+ − 165 done
+ − 166 echo "<tr><td><b>Pairs (Left & Right):</b></td></tr>" >> "$html"
+ − 167 for patient in "${pairs_Left_Right[@]}"
+ − 168 do
+ − 169 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
+ − 170 done
+ − 171 echo "<tr><td><b>Pairs (BM & PB):</b></td></tr>" >> "$html"
+ − 172 for patient in "${pairs_BM_PB[@]}"
+ − 173 do
+ − 174 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
+ − 175 done
+ − 176 echo "<tr><td><b>Pairs (Dx & R):</b></td></tr>" >> "$html"
+ − 177 for patient in "${pairs_R_Dx[@]}"
+ − 178 do
+ − 179 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
+ − 180 done
+ − 181 echo "<tr><td><b>Triplets:</b></td></tr>" >> "$html"
+ − 182
+ − 183 while read sample1 sample2 sample3
+ − 184 do
+ − 185 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
+ − 186 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
+ − 187 sample3="$(echo ${sample3} | tr -d '\r' | tr -d '\n')"
+ − 188 patient="${sample1}_${sample2}_${sample3}"
+ − 189 echo "$patient"
+ − 190 html="${patient}.html"
+ − 191 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "index.html"
1
+ − 192 echo "$header" > "$html"
0
+ − 193 oldLocus=""
1
+ − 194 tail -n+2 "${patient}_freq.txt" | sed "s/>//" > tmp.txt
0
+ − 195 echo "<div class='tabber'>" >> "$html"
+ − 196 echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
+ − 197 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
+ − 198 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
+ − 199 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>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"
+ − 200 echo "<tbody>" >> "$html"
+ − 201 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'><table border='0'><tr>"
+ − 202 while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three
+ − 203 do
+ − 204 if [ "$locus" != "$oldLocus" ] ; then
+ − 205 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>" >> "$html"
+ − 206 echo "<tr><td><b>$locus</b></td>" >> "$html"
+ − 207 else
+ − 208 echo "<td></td>" >> "$html"
+ − 209 fi
+ − 210 echo "<td>$v_segment</td>" >> "$html"
+ − 211 echo "<td>$j_segment</td>" >> "$html"
+ − 212 echo "<td>>$cut_off_value</td>" >> "$html"
+ − 213 if [ "$all" != "0" ] ; then
+ − 214 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$all</td>" >> "$html"
+ − 215 else
+ − 216 echo "<td>$all</td>" >> "$html"
+ − 217 fi
+ − 218 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 219 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> "$html"
+ − 220 else
+ − 221 echo "<td>$one</td>" >> "$html"
+ − 222 fi
+ − 223 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 224 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> "$html"
+ − 225 else
+ − 226 echo "<td>$two</td>" >> "$html"
+ − 227 fi
+ − 228 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 229 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$three</td>" >> "$html"
+ − 230 else
+ − 231 echo "<td>$three</td>" >> "$html"
+ − 232 fi
+ − 233
+ − 234 if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 235 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}freq.txt\", \"$patient\", \"freq\")'>${one_two}</td>" >> "$html"
+ − 236 else
+ − 237 echo "<td>${one_two}</td>" >> "$html"
+ − 238 fi
+ − 239 if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 240 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}freq.txt\", \"$patient\", \"freq\")'>${one_three}</td>" >> "$html"
+ − 241 else
+ − 242 echo "<td>${one_three}</td>" >> "$html"
+ − 243 fi
+ − 244 if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 245 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}freq.txt\", \"$patient\", \"freq\")'>${two_three}</td>" >> "$html"
+ − 246 else
+ − 247 echo "<td>${two_three}</td>" >> "$html"
+ − 248 fi
+ − 249
+ − 250 echo "</tr>" >> "$html"
+ − 251 oldLocus="$locus"
+ − 252 if [ "${cut_off_value}" == "0" ] ; then
+ − 253 scatterplot_tab="${scatterplot_tab}<td><img src='${sample1}_${sample2}_${sample3}_freq_${locus}_scatter.png' /></td>"
+ − 254 fi
+ − 255 done < tmp.txt
+ − 256 echo "</tbody></table>" >> "$html"
+ − 257 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html"
+ − 258 echo "</div>" >> "$html"
+ − 259 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html"
+ − 260 echo "<a href='${patient}_freq_total_all.png'><img src='${patient}_freq_total_all.png' width='1280' height='720' /></a><br />" >> "$html"
+ − 261 echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html"
+ − 262 echo "${scatterplot_tab}</tr></table></div>" >> "$html"
+ − 263
1
+ − 264 tail -n+2 "${patient}_reads.txt" | sed "s/>//" > tmp.txt
0
+ − 265 echo "<div class='tabbertab' title='Data reads'>" >> "$html"
+ − 266 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
+ − 267 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
+ − 268 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>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"
+ − 269 echo "<tbody>" >> "$html"
+ − 270 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'><table border='0'><tr>"
+ − 271 while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three
+ − 272 do
+ − 273 if [ "$locus" != "$oldLocus" ] ; then
+ − 274 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>" >> "$html"
+ − 275 echo "<tr><td><b>$locus</b></td>" >> "$html"
+ − 276 else
+ − 277 echo "<td></td>" >> "$html"
+ − 278 fi
+ − 279 echo "<td>$v_segment</td>" >> "$html"
+ − 280 echo "<td>$j_segment</td>" >> "$html"
+ − 281 echo "<td>>$cut_off_value</td>" >> "$html"
+ − 282 if [ "$all" != "0" ] ; then
+ − 283 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$all</td>" >> "$html"
+ − 284 else
+ − 285 echo "<td>$all</td>" >> "$html"
+ − 286 fi
+ − 287 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 288 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> "$html"
+ − 289 else
+ − 290 echo "<td>$one</td>" >> "$html"
+ − 291 fi
+ − 292 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 293 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> "$html"
+ − 294 else
+ − 295 echo "<td>$two</td>" >> "$html"
+ − 296 fi
+ − 297 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 298 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$three</td>" >> "$html"
+ − 299 else
+ − 300 echo "<td>$three</td>" >> "$html"
+ − 301 fi
+ − 302
+ − 303 if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 304 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}reads.txt\", \"$patient\", \"reads\")'>${one_two}</td>" >> "$html"
+ − 305 else
+ − 306 echo "<td>${one_two}</td>" >> "$html"
+ − 307 fi
+ − 308 if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 309 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}reads.txt\", \"$patient\", \"reads\")'>${one_three}</td>" >> "$html"
+ − 310 else
+ − 311 echo "<td>${one_three}</td>" >> "$html"
+ − 312 fi
+ − 313 if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+ − 314 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}reads.txt\", \"$patient\", \"reads\")'>${two_three}</td>" >> "$html"
+ − 315 else
+ − 316 echo "<td>${two_three}</td>" >> "$html"
+ − 317 fi
+ − 318
+ − 319 echo "</tr>" >> "$html"
+ − 320 oldLocus="$locus"
+ − 321 if [ "${cut_off_value}" == "0" ] ; then
+ − 322 scatterplot_tab="${scatterplot_tab}<td><img src='${sample1}_${sample2}_${sample3}_reads_${locus}_scatter.png' /></td>"
+ − 323 fi
+ − 324 done < tmp.txt
+ − 325 echo "</tbody></table>" >> "$html"
+ − 326 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html"
+ − 327 echo "</div>" >> "$html"
+ − 328 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html"
+ − 329 echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads_total_all.png' width='1280' height='720' /></a><br />" >> "$html"
+ − 330 echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html"
+ − 331 echo "${scatterplot_tab}</tr></table></div>" >> "$html"
+ − 332 echo "</div>" >> "$html"
+ − 333 echo "</div>" >> "$html"
+ − 334 echo "</html>" >> "$html"
+ − 335 done < triplets.txt
+ − 336 rm tmp.txt
+ − 337
+ − 338
+ − 339 html="index.html"
+ − 340
+ − 341 echo "</table>" >> "$html"
+ − 342 echo "<a href='log.html'>log</a><br />" >> "$html"
+ − 343 echo "<a href='single_matches.html'>single_matches</a><br />" >> "$html"
+ − 344 echo "<a href='multiple_matches.html'>multiple_matches</a><br />" >> "$html"
+ − 345 echo "</html>" >> "$html"
+ − 346
+ − 347 cp "index.html" "$outputFile"
+ − 348
