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