Mercurial > repos > mrvollger > trtr
changeset 2:b3b40009d056
Uploaded
| author | mrvollger |
|---|---|
| date | Thu, 11 Dec 2014 15:16:18 -0500 |
| parents | d734400388b1 |
| children | 2b1093ae4d0c |
| files | TRTR.git |
| diffstat | 1 files changed, 658 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TRTR.git Thu Dec 11 15:16:18 2014 -0500 @@ -0,0 +1,658 @@ + + + + +<!DOCTYPE html> +<html lang="en" class=""> + <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#"> + <meta charset='utf-8'> + <meta http-equiv="X-UA-Compatible" content="IE=edge"> + <meta http-equiv="Content-Language" content="en"> + + + <title>mvollger/TRTR ยท GitHub</title> + <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> + <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> + <link rel="apple-touch-icon" sizes="57x57" href="/apple-touch-icon-114.png"> + <link rel="apple-touch-icon" sizes="114x114" href="/apple-touch-icon-114.png"> + <link rel="apple-touch-icon" sizes="72x72" href="/apple-touch-icon-144.png"> + <link rel="apple-touch-icon" sizes="144x144" 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href="/mvollger/TRTR/tree/master" + data-name="master" + data-skip-pjax="true" + rel="nofollow" + class="js-navigation-open select-menu-item-text css-truncate-target" + title="master">master</a> + </div> <!-- /.select-menu-item --> + </div> + + <div class="select-menu-no-results">Nothing to show</div> + </div> <!-- /.select-menu-list --> + + <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="tags"> + <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> + + + </div> + + <div class="select-menu-no-results">Nothing to show</div> + </div> <!-- /.select-menu-list --> + + </div> <!-- /.select-menu-modal --> + </div> <!-- /.select-menu-modal-holder --> +</div> <!-- /.select-menu --> + + + + <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> +</div> + + + + + <div class="commit commit-tease js-details-container" > + <p class="commit-title "> + <a href="/mvollger/TRTR/commit/18ed489cf4214dad15282176452bb12ce7d91e6e" class="message" data-pjax="true" title="adding read me file">adding read me file</a> + + </p> + <div class="commit-meta"> + <button aria-label="Copy SHA" class="js-zeroclipboard zeroclipboard-link" data-clipboard-text="18ed489cf4214dad15282176452bb12ce7d91e6e" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + <a href="/mvollger/TRTR/commit/18ed489cf4214dad15282176452bb12ce7d91e6e" class="sha-block" data-pjax>latest commit <span class="sha">18ed489cf4</span></a> + + <div class="authorship"> + <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" /> + <span class="author-name"><a href="/mvollger" rel="author">mvollger</a></span> + authored <time class="updated" datetime="2014-12-11T19:58:37Z" is="relative-time">Dec 11, 2014</time> + + </div> + </div> + </div> + + +<div class="file-wrap"> + + <table class="files" data-pjax> + + + <tbody> + <tr class="warning include-fragment-error"> + <td class="icon"><span class="octicon octicon-alert"></span></td> + <td class="content" colspan="3">Failed to load latest commit information.</td> + </tr> + + <tr> + <td class="icon"> + <span class="octicon octicon-file-directory"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> + </td> + <td class="content"> + <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> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <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> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2014-12-11T19:47:00Z" is="time-ago">Dec 11, 2014</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> + </td> + <td class="content"> + <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> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/mvollger/TRTR/commit/18ed489cf4214dad15282176452bb12ce7d91e6e" class="message" data-pjax="true" title="adding read me file">adding read me file</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2014-12-11T19:58:37Z" is="time-ago">Dec 11, 2014</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a 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id="3f948a8def2551323bf8ad1ba9dd2957-b5e365802398ae2a924593aab6bf86237ea269c0" title="trtr.c">trtr.c</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <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> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2014-12-11T19:47:00Z" is="time-ago">Dec 11, 2014</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> + </td> + <td class="content"> + <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> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <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> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2014-12-11T19:47:00Z" is="time-ago">Dec 11, 2014</time></span> + </td> + </tr> + </tbody> + </table> + +</div> + + + <div id="readme" class="boxed-group flush clearfix announce instapaper_body md"> + <h3> + <span class="octicon octicon-book"></span> + README.md + </h3> + + <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> + +<p>The maximimum repeat length is adjustable (use 1 to trim only homopolymers).</p> + +<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> + +<p>This could also be a useful first step before assembly. More testing needs to be done.</p> +</article> + </div> + + + </div> + + </div><!-- /.repo-container --> + <div class="modal-backdrop"></div> + </div><!-- /.container --> + </div><!-- /.site --> + + + </div><!-- /.wrapper --> + + <div class="container"> + <div class="site-footer" role="contentinfo"> + <ul class="site-footer-links right"> + <li><a href="https://status.github.com/">Status</a></li> + <li><a href="https://developer.github.com">API</a></li> + <li><a href="http://training.github.com">Training</a></li> + <li><a href="http://shop.github.com">Shop</a></li> + <li><a href="/blog">Blog</a></li> + <li><a href="/about">About</a></li> + + </ul> + + <a href="/" aria-label="Homepage"> + <span class="mega-octicon octicon-mark-github" title="GitHub"></span> + </a> + + <ul class="site-footer-links"> + <li>© 2014 <span title="0.03013s from github-fe124-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> + <li><a href="/site/terms">Terms</a></li> + <li><a href="/site/privacy">Privacy</a></li> + <li><a href="/security">Security</a></li> + <li><a href="/contact">Contact</a></li> + </ul> + </div><!-- /.site-footer --> +</div><!-- /.container --> + + + <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay"> + <div class="fullscreen-container js-suggester-container"> + <div class="textarea-wrap"> + <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder=""></textarea> + <div class="suggester-container"> + <div class="suggester fullscreen-suggester js-suggester js-navigation-container"></div> + </div> + </div> + </div> + <div class="fullscreen-sidebar"> + <a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode"> + <span class="mega-octicon octicon-screen-normal"></span> + </a> + <a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w" + aria-label="Switch themes"> + <span class="octicon octicon-color-mode"></span> + </a> + </div> +</div> + + + + <div id="ajax-error-message" class="flash flash-error"> + <span class="octicon octicon-alert"></span> + <a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a> + Something went wrong with that request. 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