Mercurial > repos > mrvollger > trtr
changeset 3:2b1093ae4d0c
Deleted selected files
| author | mrvollger |
|---|---|
| date | Thu, 11 Dec 2014 15:19:53 -0500 |
| parents | b3b40009d056 |
| children | 8e680796e3ff |
| files | TRTR TRTR.git |
| diffstat | 2 files changed, 0 insertions(+), 1316 deletions(-) [+] |
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--- a/TRTR Thu Dec 11 15:16:18 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,658 +0,0 @@ - - - - -<!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" href="/apple-touch-icon-144.png"> - 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<ol class="repository-lang-stats-numbers"> - <li> - <a href="/mvollger/TRTR/search?l=c"> - <span class="color-block language-color" style="background-color:#555;"></span> - <span class="lang">C</span> - <span class="percent">100%</span> - </a> - </li> - </ol> - </div> - </div> - </div> - -</div> - - <div class="tooltipped tooltipped-s" aria-label="Show language statistics"> - <a href="#" - class="repository-lang-stats-graph js-toggle-lang-stats" - style="background-color:#555"> - <span class="language-color" style="width:100%; background-color:#555;" itemprop="keywords">C</span> - </a> - </div> - -<include-fragment src="/mvollger/TRTR/show_partial?partial=recently_touched_branches_list"></include-fragment> - -<div class="file-navigation in-mid-page"> - <a href="/mvollger/TRTR/find/master" - class="js-show-file-finder minibutton empty-icon tooltipped tooltipped-s right" - data-pjax - data-hotkey="t" - aria-label="Quickly jump between files"> - <span class="octicon octicon-list-unordered"></span> - 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</div> <!-- /.select-menu-header --> - - <div class="select-menu-filters"> - <div class="select-menu-text-filter"> - <input type="text" aria-label="Filter branches/tags" id="context-commitish-filter-field" class="js-filterable-field js-navigation-enable" placeholder="Filter branches/tags"> - </div> - <div class="select-menu-tabs"> - <ul> - <li class="select-menu-tab"> - <a href="#" data-tab-filter="branches" class="js-select-menu-tab">Branches</a> - </li> - <li class="select-menu-tab"> - <a href="#" data-tab-filter="tags" class="js-select-menu-tab">Tags</a> - </li> - </ul> - </div><!-- /.select-menu-tabs --> - </div><!-- /.select-menu-filters --> - - <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches"> - - <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> - - - <div class="select-menu-item js-navigation-item selected"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <a 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> - 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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. 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</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. 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