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7 <head prefix="og: http://ogp.me/ns# fb: http://ogp.me/ns/fb# object: http://ogp.me/ns/object# article: http://ogp.me/ns/article# profile: http://ogp.me/ns/profile#">
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11
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12
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13 <title>mvollger/TRTR ยท GitHub</title>
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14 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub">
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23 <meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="https://avatars1.githubusercontent.com/u/6935283?v=3&s=400" property="og:image" /><meta content="mvollger/TRTR" property="og:title" /><meta content="https://github.com/mvollger/TRTR" property="og:url" /><meta content="Contribute to TRTR development by creating an account on GitHub." property="og:description" />
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24
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25 <meta name="browser-stats-url" content="/_stats">
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26 <link rel="assets" href="https://assets-cdn.github.com/">
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39 <meta content="Rails, view, files#disambiguate" name="analytics-event" />
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43 <link rel="icon" type="image/x-icon" href="https://assets-cdn.github.com/favicon.ico">
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46 <meta content="authenticity_token" name="csrf-param" />
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49 <link href="https://assets-cdn.github.com/assets/github-c7f434a471766a748d862b4cb294526acd6901321d901cc64028f53af8490603.css" media="all" rel="stylesheet" type="text/css" />
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50 <link href="https://assets-cdn.github.com/assets/github2-d3255e3762ec73006730d22d2db05bd45c6ba29468f8808e238c160550ca87ef.css" media="all" rel="stylesheet" type="text/css" />
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55 <meta http-equiv="x-pjax-version" content="38cf36b78efb25a234c35bc9b920031d">
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56
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57
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58 <meta name="description" content="Contribute to TRTR development by creating an account on GitHub.">
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59 <meta name="go-import" content="github.com/mvollger/TRTR git https://github.com/mvollger/TRTR.git">
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60
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61 <meta content="6935283" name="octolytics-dimension-user_id" /><meta content="mvollger" name="octolytics-dimension-user_login" /><meta content="27889006" name="octolytics-dimension-repository_id" /><meta content="mvollger/TRTR" name="octolytics-dimension-repository_nwo" /><meta content="true" name="octolytics-dimension-repository_public" /><meta content="false" name="octolytics-dimension-repository_is_fork" /><meta content="27889006" name="octolytics-dimension-repository_network_root_id" /><meta content="mvollger/TRTR" name="octolytics-dimension-repository_network_root_nwo" />
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62 <link href="https://github.com/mvollger/TRTR/commits/master.atom" rel="alternate" title="Recent Commits to TRTR:master" type="application/atom+xml">
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63
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64 </head>
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65
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66
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67 <body class="logged_out env-production vis-public">
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68 <a href="#start-of-content" tabindex="1" class="accessibility-aid js-skip-to-content">Skip to content</a>
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69 <div class="wrapper">
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77 <div class="header header-logged-out" role="banner">
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78 <div class="container clearfix">
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79
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80 <a class="header-logo-wordmark" href="https://github.com/" ga-data-click="(Logged out) Header, go to homepage, icon:logo-wordmark">
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81 <span class="mega-octicon octicon-logo-github"></span>
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82 </a>
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83
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84 <div class="header-actions" role="navigation">
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85 <a class="button primary" href="/join" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up">Sign up</a>
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86 <a class="button" href="/login?return_to=%2Fmvollger%2FTRTR" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in">Sign in</a>
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87 </div>
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88
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89 <div class="site-search repo-scope js-site-search" role="search">
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90 <form accept-charset="UTF-8" action="/mvollger/TRTR/search" class="js-site-search-form" data-global-search-url="/search" data-repo-search-url="/mvollger/TRTR/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div>
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91 <input type="text"
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92 class="js-site-search-field is-clearable"
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93 data-hotkey="s"
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94 name="q"
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95 placeholder="Search"
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96 data-global-scope-placeholder="Search GitHub"
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97 data-repo-scope-placeholder="Search"
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98 tabindex="1"
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99 autocapitalize="off">
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100 <div class="scope-badge">This repository</div>
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101 </form>
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102 </div>
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103
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104 <ul class="header-nav left" role="navigation">
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105 <li class="header-nav-item">
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106 <a class="header-nav-link" href="/explore" data-ga-click="(Logged out) Header, go to explore, text:explore">Explore</a>
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107 </li>
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108 <li class="header-nav-item">
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109 <a class="header-nav-link" href="/features" data-ga-click="(Logged out) Header, go to features, text:features">Features</a>
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110 </li>
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111 <li class="header-nav-item">
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112 <a class="header-nav-link" href="https://enterprise.github.com/" data-ga-click="(Logged out) Header, go to enterprise, text:enterprise">Enterprise</a>
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113 </li>
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114 <li class="header-nav-item">
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115 <a class="header-nav-link" href="/blog" data-ga-click="(Logged out) Header, go to blog, text:blog">Blog</a>
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116 </li>
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117 </ul>
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118
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119 </div>
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120 </div>
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121
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122
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123
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124 <div id="start-of-content" class="accessibility-aid"></div>
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125 <div class="site" itemscope itemtype="http://schema.org/WebPage">
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126 <div id="js-flash-container">
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127
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128 </div>
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129 <div class="pagehead repohead instapaper_ignore readability-menu">
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130 <div class="container">
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131
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132 <ul class="pagehead-actions">
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133
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134
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135 <li>
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136 <a href="/login?return_to=%2Fmvollger%2FTRTR"
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137 class="minibutton with-count star-button tooltipped tooltipped-n"
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138 aria-label="You must be signed in to star a repository" rel="nofollow">
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139 <span class="octicon octicon-star"></span>
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140 Star
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141 </a>
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142
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143 <a class="social-count js-social-count" href="/mvollger/TRTR/stargazers">
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144 0
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145 </a>
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146
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147 </li>
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148
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149 <li>
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150 <a href="/login?return_to=%2Fmvollger%2FTRTR"
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151 class="minibutton with-count js-toggler-target fork-button tooltipped tooltipped-n"
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152 aria-label="You must be signed in to fork a repository" rel="nofollow">
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153 <span class="octicon octicon-repo-forked"></span>
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154 Fork
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155 </a>
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156 <a href="/mvollger/TRTR/network" class="social-count">
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157 0
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158 </a>
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159 </li>
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160 </ul>
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161
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162 <h1 itemscope itemtype="http://data-vocabulary.org/Breadcrumb" class="entry-title public">
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163 <span class="mega-octicon octicon-repo"></span>
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164 <span class="author"><a href="/mvollger" class="url fn" itemprop="url" rel="author"><span itemprop="title">mvollger</span></a></span><!--
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165 --><span class="path-divider">/</span><!--
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166 --><strong><a href="/mvollger/TRTR" class="js-current-repository" data-pjax="#js-repo-pjax-container">TRTR</a></strong>
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167
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168 <span class="page-context-loader">
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169 <img alt="" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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170 </span>
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171
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172 </h1>
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173 </div><!-- /.container -->
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174 </div><!-- /.repohead -->
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175
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176 <div class="container">
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177 <div class="repository-with-sidebar repo-container new-discussion-timeline with-full-navigation ">
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178 <div class="repository-sidebar clearfix">
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179
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180 <nav class="sunken-menu repo-nav js-repo-nav js-sidenav-container-pjax js-octicon-loaders"
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181 role="navigation"
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182 data-pjax="#js-repo-pjax-container"
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183 data-issue-count-url="/mvollger/TRTR/issues/counts">
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184 <ul class="sunken-menu-group">
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185 <li class="tooltipped tooltipped-w" aria-label="Code">
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186 <a href="/mvollger/TRTR" aria-label="Code" class="selected js-selected-navigation-item sunken-menu-item" data-hotkey="g c" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /mvollger/TRTR">
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187 <span class="octicon octicon-code"></span> <span class="full-word">Code</span>
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188 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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189 </a> </li>
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190
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191 <li class="tooltipped tooltipped-w" aria-label="Issues">
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192 <a href="/mvollger/TRTR/issues" aria-label="Issues" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g i" data-selected-links="repo_issues repo_labels repo_milestones /mvollger/TRTR/issues">
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193 <span class="octicon octicon-issue-opened"></span> <span class="full-word">Issues</span>
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194 <span class="js-issue-replace-counter"></span>
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195 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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196 </a> </li>
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197
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198 <li class="tooltipped tooltipped-w" aria-label="Pull Requests">
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199 <a href="/mvollger/TRTR/pulls" aria-label="Pull Requests" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g p" data-selected-links="repo_pulls /mvollger/TRTR/pulls">
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200 <span class="octicon octicon-git-pull-request"></span> <span class="full-word">Pull Requests</span>
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201 <span class="js-pull-replace-counter"></span>
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202 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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203 </a> </li>
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204
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205
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206 </ul>
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207 <div class="sunken-menu-separator"></div>
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208 <ul class="sunken-menu-group">
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209
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210 <li class="tooltipped tooltipped-w" aria-label="Pulse">
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211 <a href="/mvollger/TRTR/pulse" aria-label="Pulse" class="js-selected-navigation-item sunken-menu-item" data-selected-links="pulse /mvollger/TRTR/pulse">
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212 <span class="octicon octicon-pulse"></span> <span class="full-word">Pulse</span>
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213 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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214 </a> </li>
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215
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216 <li class="tooltipped tooltipped-w" aria-label="Graphs">
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217 <a href="/mvollger/TRTR/graphs" aria-label="Graphs" class="js-selected-navigation-item sunken-menu-item" data-selected-links="repo_graphs repo_contributors /mvollger/TRTR/graphs">
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218 <span class="octicon octicon-graph"></span> <span class="full-word">Graphs</span>
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219 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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220 </a> </li>
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221 </ul>
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222
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223
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224 </nav>
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225
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226 <div class="only-with-full-nav">
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227
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228
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229 <div class="clone-url open"
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230 data-protocol-type="http"
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231 data-url="/users/set_protocol?protocol_selector=http&protocol_type=clone">
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232 <h3><span class="text-emphasized">HTTPS</span> clone URL</h3>
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233 <div class="input-group js-zeroclipboard-container">
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234 <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
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235 value="https://github.com/mvollger/TRTR.git" readonly="readonly">
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236 <span class="input-group-button">
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237 <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
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238 </span>
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239 </div>
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240 </div>
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241
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242
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243 <div class="clone-url "
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244 data-protocol-type="subversion"
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245 data-url="/users/set_protocol?protocol_selector=subversion&protocol_type=clone">
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246 <h3><span class="text-emphasized">Subversion</span> checkout URL</h3>
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247 <div class="input-group js-zeroclipboard-container">
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248 <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
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249 value="https://github.com/mvollger/TRTR" readonly="readonly">
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250 <span class="input-group-button">
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251 <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
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252 </span>
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253 </div>
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254 </div>
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255
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256
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257
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258 <p class="clone-options">You can clone with
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259 <a href="#" class="js-clone-selector" data-protocol="http">HTTPS</a> or <a href="#" class="js-clone-selector" data-protocol="subversion">Subversion</a>.
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260 <a href="https://help.github.com/articles/which-remote-url-should-i-use" class="help tooltipped tooltipped-n" aria-label="Get help on which URL is right for you.">
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261 <span class="octicon octicon-question"></span>
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262 </a>
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263 </p>
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264
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265
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266
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267 <a href="/mvollger/TRTR/archive/master.zip"
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268 class="minibutton sidebar-button"
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269 aria-label="Download the contents of mvollger/TRTR as a zip file"
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270 title="Download the contents of mvollger/TRTR as a zip file"
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271 rel="nofollow">
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272 <span class="octicon octicon-cloud-download"></span>
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273 Download ZIP
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274 </a>
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275 </div>
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276 </div><!-- /.repository-sidebar -->
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277
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278 <div id="js-repo-pjax-container" class="repository-content context-loader-container" data-pjax-container>
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279
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280 <span id="js-show-full-navigation"></span>
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281
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282 <div class="repository-meta js-details-container ">
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283
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284
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285
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286 </div>
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287
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288 <div class="overall-summary overall-summary-bottomless">
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289
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290 <div class="stats-switcher-viewport js-stats-switcher-viewport">
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291 <div class="stats-switcher-wrapper">
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292 <ul class="numbers-summary">
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293 <li class="commits">
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294 <a data-pjax href="/mvollger/TRTR/commits/master">
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295 <span class="octicon octicon-history"></span>
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296 <span class="num text-emphasized">
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297 2
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298 </span>
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299 commits
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300 </a>
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301 </li>
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302 <li>
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303 <a data-pjax href="/mvollger/TRTR/branches">
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439
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440
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441
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442 <div class="breadcrumb"><span class='repo-root js-repo-root'><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/mvollger/TRTR" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">TRTR</span></a></span></span><span class="separator">/</span><form action="/login?return_to=%2Fmvollger%2FTRTR" aria-label="Sign in to make or propose changes" class="js-new-blob-form tooltipped tooltipped-e new-file-link" method="post"><span aria-label="Sign in to make or propose changes" class="js-new-blob-submit octicon octicon-plus" data-test-id="create-new-git-file" role="button"></span></form></div>
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443 </div>
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451
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455 <a href="/mvollger/TRTR/commit/18ed489cf4214dad15282176452bb12ce7d91e6e" class="sha-block" data-pjax>latest commit <span class="sha">18ed489cf4</span></a>
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456
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457 <div class="authorship">
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458 <img alt="Mitchell Robert Vollger" class="avatar" data-user="6935283" height="20" src="https://avatars1.githubusercontent.com/u/6935283?v=3&s=40" width="20" />
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459 <span class="author-name"><a href="/mvollger" rel="author">mvollger</a></span>
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460 authored <time class="updated" datetime="2014-12-11T19:58:37Z" is="relative-time">Dec 11, 2014</time>
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461
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462 </div>
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463 </div>
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464 </div>
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468
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472 <tbody>
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474 <td class="icon"><span class="octicon octicon-alert"></span></td>
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475 <td class="content" colspan="3">Failed to load latest commit information.</td>
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476 </tr>
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481 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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482 </td>
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484 <span class="css-truncate css-truncate-target"><a href="/mvollger/TRTR/tree/master/test-data" class="js-directory-link" id="24346e1b50066607059af36e3b684b24-64040d5e28d23bf856cc984baa54d429d95fc7c7" title="test-data">test-data</a></span>
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485 </td>
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486 <td class="message">
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487 <span class="css-truncate css-truncate-target">
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488 <a href="/mvollger/TRTR/commit/4b01881bee84344a00dda0a52e4d8f61f6817e08" class="message" data-pjax="true" title="This is version 1.00 of TRTR">This is version 1.00 of TRTR</a>
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489 </span>
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490 </td>
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491 <td class="age">
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492 <span class="css-truncate css-truncate-target"><time datetime="2014-12-11T19:47:00Z" is="time-ago">Dec 11, 2014</time></span>
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493 </td>
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494 </tr>
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495 <tr>
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498 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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499 </td>
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500 <td class="content">
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501 <span class="css-truncate css-truncate-target"><a href="/mvollger/TRTR/blob/master/README.md" class="js-directory-link" id="04c6e90faac2675aa89e2176d2eec7d8-1078740a0afb61b2ac8a8928fae3c4f467eaf7d3" title="README.md">README.md</a></span>
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502 </td>
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503 <td class="message">
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504 <span class="css-truncate css-truncate-target">
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505 <a href="/mvollger/TRTR/commit/18ed489cf4214dad15282176452bb12ce7d91e6e" class="message" data-pjax="true" title="adding read me file">adding read me file</a>
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506 </span>
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507 </td>
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508 <td class="age">
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509 <span class="css-truncate css-truncate-target"><time datetime="2014-12-11T19:58:37Z" is="time-ago">Dec 11, 2014</time></span>
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510 </td>
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511 </tr>
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512 <tr>
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515 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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516 </td>
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517 <td class="content">
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518 <span class="css-truncate css-truncate-target"><a href="/mvollger/TRTR/blob/master/trtr" class="js-directory-link" id="df09e6b25ae335febd8ba69ee7daa07b-b1f0986d238b8f2bf2a57ba23814641c1a3726bd" title="trtr">trtr</a></span>
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519 </td>
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520 <td class="message">
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521 <span class="css-truncate css-truncate-target">
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522 <a href="/mvollger/TRTR/commit/4b01881bee84344a00dda0a52e4d8f61f6817e08" class="message" data-pjax="true" title="This is version 1.00 of TRTR">This is version 1.00 of TRTR</a>
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523 </span>
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524 </td>
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525 <td class="age">
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526 <span class="css-truncate css-truncate-target"><time datetime="2014-12-11T19:47:00Z" is="time-ago">Dec 11, 2014</time></span>
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527 </td>
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528 </tr>
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529 <tr>
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533 </td>
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534 <td class="content">
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535 <span class="css-truncate css-truncate-target"><a href="/mvollger/TRTR/blob/master/trtr.c" class="js-directory-link" id="3f948a8def2551323bf8ad1ba9dd2957-b5e365802398ae2a924593aab6bf86237ea269c0" title="trtr.c">trtr.c</a></span>
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536 </td>
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537 <td class="message">
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538 <span class="css-truncate css-truncate-target">
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539 <a href="/mvollger/TRTR/commit/4b01881bee84344a00dda0a52e4d8f61f6817e08" class="message" data-pjax="true" title="This is version 1.00 of TRTR">This is version 1.00 of TRTR</a>
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540 </span>
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541 </td>
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542 <td class="age">
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543 <span class="css-truncate css-truncate-target"><time datetime="2014-12-11T19:47:00Z" is="time-ago">Dec 11, 2014</time></span>
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544 </td>
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545 </tr>
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546 <tr>
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549 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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550 </td>
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551 <td class="content">
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552 <span class="css-truncate css-truncate-target"><a href="/mvollger/TRTR/blob/master/trtr.xml" class="js-directory-link" id="b685bffece7725218c6fa590c543d117-60edbbaaac3eff80f7faeb7ddeca00e53883d253" title="trtr.xml">trtr.xml</a></span>
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553 </td>
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554 <td class="message">
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555 <span class="css-truncate css-truncate-target">
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556 <a href="/mvollger/TRTR/commit/4b01881bee84344a00dda0a52e4d8f61f6817e08" class="message" data-pjax="true" title="This is version 1.00 of TRTR">This is version 1.00 of TRTR</a>
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557 </span>
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558 </td>
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559 <td class="age">
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560 <span class="css-truncate css-truncate-target"><time datetime="2014-12-11T19:47:00Z" is="time-ago">Dec 11, 2014</time></span>
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561 </td>
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562 </tr>
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563 </tbody>
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564 </table>
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565
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566 </div>
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567
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568
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569 <div id="readme" class="boxed-group flush clearfix announce instapaper_body md">
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570 <h3>
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571 <span class="octicon octicon-book"></span>
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572 README.md
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573 </h3>
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574
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575 <article class="markdown-body entry-content" itemprop="mainContentOfPage"><p>This tool removes tandem repeats from ends of unaligned sequencing reads (leaving one copy). This prevents reads that don't span the repeated region from overlapping and leading to innaccurate SNPs calls.</p>
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576
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577 <p>The maximimum repeat length is adjustable (use 1 to trim only homopolymers).</p>
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578
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579 <p>The "aggressive" option should not be touched in general. Setting to 0 will prevent the program from trimming to exactly 1 copy of the repeat, instead leaving between 1 and 2 copies.</p>
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580
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581 <p>This could also be a useful first step before assembly. More testing needs to be done.</p>
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582 </article>
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583 </div>
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584
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585
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586 </div>
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587
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588 </div><!-- /.repo-container -->
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589 <div class="modal-backdrop"></div>
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590 </div><!-- /.container -->
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591 </div><!-- /.site -->
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592
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593
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594 </div><!-- /.wrapper -->
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595
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596 <div class="container">
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597 <div class="site-footer" role="contentinfo">
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598 <ul class="site-footer-links right">
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599 <li><a href="https://status.github.com/">Status</a></li>
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600 <li><a href="https://developer.github.com">API</a></li>
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601 <li><a href="http://training.github.com">Training</a></li>
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602 <li><a href="http://shop.github.com">Shop</a></li>
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603 <li><a href="/blog">Blog</a></li>
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604 <li><a href="/about">About</a></li>
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605
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606 </ul>
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607
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608 <a href="/" aria-label="Homepage">
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609 <span class="mega-octicon octicon-mark-github" title="GitHub"></span>
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610 </a>
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611
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612 <ul class="site-footer-links">
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1
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613 <li>© 2014 <span title="0.03599s from github-fe130-cp1-prd.iad.github.net">GitHub</span>, Inc.</li>
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614 <li><a href="/site/terms">Terms</a></li>
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615 <li><a href="/site/privacy">Privacy</a></li>
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616 <li><a href="/security">Security</a></li>
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617 <li><a href="/contact">Contact</a></li>
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618 </ul>
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619 </div><!-- /.site-footer -->
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620 </div><!-- /.container -->
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621
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622
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623 <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay">
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624 <div class="fullscreen-container js-suggester-container">
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625 <div class="textarea-wrap">
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626 <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder=""></textarea>
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627 <div class="suggester-container">
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628 <div class="suggester fullscreen-suggester js-suggester js-navigation-container"></div>
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629 </div>
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630 </div>
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631 </div>
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632 <div class="fullscreen-sidebar">
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633 <a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode">
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634 <span class="mega-octicon octicon-screen-normal"></span>
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635 </a>
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636 <a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w"
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637 aria-label="Switch themes">
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638 <span class="octicon octicon-color-mode"></span>
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639 </a>
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640 </div>
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641 </div>
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642
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643
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644
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645 <div id="ajax-error-message" class="flash flash-error">
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646 <span class="octicon octicon-alert"></span>
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647 <a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a>
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648 Something went wrong with that request. Please try again.
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649 </div>
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650
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651
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652 <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-153d6254b838872c8db73c8bd92905913f6f5b2164b7e40e5292286bd5a39403.js" type="text/javascript"></script>
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653 <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-9aff85b0c22df0388606ce23a0388d77fa84e66682852b08f63fbe461410d999.js" type="text/javascript"></script>
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654
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655
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656 </body>
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657 </html>
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658
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