Mercurial > repos > lz_hust > gatktools
diff gatk-tools @ 6:a4e5c90cf6cb draft
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| author | lz_hust |
|---|---|
| date | Sat, 01 Jun 2019 07:03:27 -0400 |
| parents | |
| children |
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13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> +</li> + +</ul> + +<ul class="d-none js-jump-to-no-results-template-container"> + <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2"> + <span class="text-gray">No suggested jump to results</span> + </li> +</ul> + +<ul id="jump-to-results" role="listbox" class="p-0 m-0 js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container"> + + +<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-scoped-search d-none" role="option"> + <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> + <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> + <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> + <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> + <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> +</li> + + + +<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option"> + <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> + <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> + <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> + <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> + <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> +</li> + + +</ul> + + </div> + </label> +</form> </div> +</div> + + </div> + + <a class="HeaderMenu-link no-underline mr-3" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"9296:3F63:B1FBFC:1321364:5CF25B7F","originating_url":"https://github.com/huster16/gatk-tools","referrer":null,"user_id":null}}" data-hydro-click-hmac="fd39d520055d8446e558ee9e8a4559fcf3c2707ff08aa36af3730909059570dd" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in" href="/login?return_to=%2Fhuster16%2Fgatk-tools"> + Sign in +</a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"9296:3F63:B1FBFC:1321364:5CF25B7F","originating_url":"https://github.com/huster16/gatk-tools","referrer":null,"user_id":null}}" data-hydro-click-hmac="64c8aa9f44411d6847c02cf39127ae3a325a4d3950eccd853bc3d3d21f56be63" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join"> + Sign up +</a> </div> + </div> + </div> +</header> + + </div> + + <div id="start-of-content" class="show-on-focus"></div> + + + <div id="js-flash-container"> + +</div> + + + + <div class="application-main " data-commit-hovercards-enabled> + <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class=""> + <main id="js-repo-pjax-container" data-pjax-container > + + + + + + + + + <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav "> + <div class="repohead-details-container clearfix container"> + + <ul class="pagehead-actions"> + + + + + <li> + + <a class="tooltipped tooltipped-s btn btn-sm btn-with-count" aria-label="You must be signed in to watch a repository" rel="nofollow" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"notification subscription menu watch","repository_id":null,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"9296:3F63:B1FBFC:1321364:5CF25B7F","originating_url":"https://github.com/huster16/gatk-tools","referrer":null,"user_id":null}}" data-hydro-click-hmac="dbd991e234ce46fc4f62b3bc77da0c3873ee09a32e84f05236c983f8ec38e576" href="/login?return_to=%2Fhuster16%2Fgatk-tools"> + <svg class="octicon octicon-eye v-align-text-bottom" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.06 2C3 2 0 8 0 8s3 6 8.06 6C13 14 16 8 16 8s-3-6-7.94-6zM8 12c-2.2 0-4-1.78-4-4 0-2.2 1.8-4 4-4 2.22 0 4 1.8 4 4 0 2.22-1.78 4-4 4zm2-4c0 1.11-.89 2-2 2-1.11 0-2-.89-2-2 0-1.11.89-2 2-2 1.11 0 2 .89 2 2z"/></svg> + Watch +</a> <a class="social-count" href="/huster16/gatk-tools/watchers" + aria-label="0 users are watching this repository"> + 0 + </a> + + </li> + + <li> + <a class="btn btn-sm btn-with-count tooltipped tooltipped-s" aria-label="You must be signed in to star a repository" rel="nofollow" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"star button","repository_id":189599350,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"9296:3F63:B1FBFC:1321364:5CF25B7F","originating_url":"https://github.com/huster16/gatk-tools","referrer":null,"user_id":null}}" data-hydro-click-hmac="7bed868485937510b69e0bc19d11023a5a1cc70d3d2d2036be837e66372ba7a0" href="/login?return_to=%2Fhuster16%2Fgatk-tools"> + <svg class="octicon octicon-star v-align-text-bottom" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M14 6l-4.9-.64L7 1 4.9 5.36 0 6l3.6 3.26L2.67 14 7 11.67 11.33 14l-.93-4.74L14 6z"/></svg> + Star +</a> + <a class="social-count js-social-count" href="/huster16/gatk-tools/stargazers" + aria-label="0 users starred this repository"> + 0 + </a> + + </li> + + <li> + <a class="btn btn-sm btn-with-count tooltipped tooltipped-s" aria-label="You must be signed in to fork a repository" rel="nofollow" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"repo details fork button","repository_id":189599350,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"9296:3F63:B1FBFC:1321364:5CF25B7F","originating_url":"https://github.com/huster16/gatk-tools","referrer":null,"user_id":null}}" data-hydro-click-hmac="b471484d807715f3d9e3791444007693482a90517d741978272abdc02d7df366" href="/login?return_to=%2Fhuster16%2Fgatk-tools"> + <svg class="octicon octicon-repo-forked v-align-text-bottom" viewBox="0 0 10 16" version="1.1" width="10" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8 1a1.993 1.993 0 0 0-1 3.72V6L5 8 3 6V4.72A1.993 1.993 0 0 0 2 1a1.993 1.993 0 0 0-1 3.72V6.5l3 3v1.78A1.993 1.993 0 0 0 5 15a1.993 1.993 0 0 0 1-3.72V9.5l3-3V4.72A1.993 1.993 0 0 0 8 1zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3 10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3-10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg> + Fork +</a> + <a href="/huster16/gatk-tools/network/members" class="social-count" + aria-label="0 users forked this repository"> + 0 + </a> + </li> +</ul> + + <h1 class="public "> + <svg class="octicon octicon-repo" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> + <span class="author" itemprop="author"><a class="url fn" rel="author" data-hovercard-type="user" data-hovercard-url="/hovercards?user_id=50308301" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/huster16">huster16</a></span><!-- +--><span class="path-divider">/</span><!-- +--><strong itemprop="name"><a data-pjax="#js-repo-pjax-container" href="/huster16/gatk-tools">gatk-tools</a></strong> + + +</h1> + + </div> + +<nav class="hx_reponav reponav js-repo-nav js-sidenav-container-pjax container" + itemscope + itemtype="http://schema.org/BreadcrumbList" + aria-label="Repository" + data-pjax="#js-repo-pjax-container"> + + <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> + <a class="js-selected-navigation-item selected reponav-item" itemprop="url" data-hotkey="g c" aria-current="page" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches repo_packages /huster16/gatk-tools" href="/huster16/gatk-tools"> + <svg class="octicon octicon-code" viewBox="0 0 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class="css-truncate-target">master</span> + </summary> + + <details-menu class="select-menu-modal hx_rsm-modal position-absolute" style="z-index: 99;" src="/huster16/gatk-tools/ref-list/master?source_action=disambiguate&source_controller=files" preload> + <include-fragment class="select-menu-loading-overlay anim-pulse"> + <svg height="32" class="octicon octicon-octoface" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M14.7 5.34c.13-.32.55-1.59-.13-3.31 0 0-1.05-.33-3.44 1.3-1-.28-2.07-.32-3.13-.32s-2.13.04-3.13.32c-2.39-1.64-3.44-1.3-3.44-1.3-.68 1.72-.26 2.99-.13 3.31C.49 6.21 0 7.33 0 8.69 0 13.84 3.33 15 7.98 15S16 13.84 16 8.69c0-1.36-.49-2.48-1.3-3.35zM8 14.02c-3.3 0-5.98-.15-5.98-3.35 0-.76.38-1.48 1.02-2.07 1.07-.98 2.9-.46 4.96-.46 2.07 0 3.88-.52 4.96.46.65.59 1.02 1.3 1.02 2.07 0 3.19-2.68 3.35-5.98 3.35zM5.49 9.01c-.66 0-1.2.8-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.54-1.78-1.2-1.78zm5.02 0c-.66 0-1.2.79-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.53-1.78-1.2-1.78z"/></svg> + </include-fragment> + </details-menu> +</details> + + + <button type="button" class="btn btn-sm disabled tooltipped tooltipped-n new-pull-request-btn" aria-label="You must be signed in to create a pull request"> + New pull request + </button> + + <div class="breadcrumb flex-auto"> + + </div> + + <div class="BtnGroup"> + + <a class="btn btn-sm empty-icon float-right BtnGroup-item" data-hydro-click="{"event_type":"repository.click","payload":{"target":"FIND_FILE_BUTTON","repository_id":189599350,"client_id":null,"originating_request_id":"9296:3F63:B1FBFC:1321364:5CF25B7F","originating_url":"https://github.com/huster16/gatk-tools","referrer":null,"user_id":null}}" data-hydro-click-hmac="2202b3ffe5544f8163f8b93af3713fc7029c4f471879a84fe8f338309f52faab" data-ga-click="Repository, find file, location:repo overview" data-hotkey="t" data-pjax="true" href="/huster16/gatk-tools/find/master">Find File</a> + </div> + + + + + <details class="get-repo-select-menu js-get-repo-select-menu js-anon-get-repo-select-menu position-relative details-overlay details-reset"> + <summary class="btn btn-sm ml-2 btn-primary" data-hydro-click="{"event_type":"repository.click","payload":{"repository_id":189599350,"target":"CLONE_OR_DOWNLOAD_BUTTON","client_id":null,"originating_request_id":"9296:3F63:B1FBFC:1321364:5CF25B7F","originating_url":"https://github.com/huster16/gatk-tools","referrer":null,"user_id":null}}" data-hydro-click-hmac="4525d521fa4701080dc4256fee3f654f20406206ba9f433f0e4d0b3ce8e26964"> + Clone or download + <span class="dropdown-caret"></span> +</summary> <div class="position-relative"> + <div class="get-repo-modal dropdown-menu dropdown-menu-sw pb-0 js-toggler-container js-get-repo-modal"> + + <div class="get-repo-modal-options"> + <div class="clone-options https-clone-options"> + + <h4 class="mb-1"> + Clone with HTTPS + <a class="muted-link" href="https://help.github.com/articles/which-remote-url-should-i-use" target="_blank" title="Which remote URL should I use?"> + <svg class="octicon octicon-question" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M6 10h2v2H6v-2zm4-3.5C10 8.64 8 9 8 9H6c0-.55.45-1 1-1h.5c.28 0 .5-.22.5-.5v-1c0-.28-.22-.5-.5-.5h-1c-.28 0-.5.22-.5.5V7H4c0-1.5 1.5-3 3-3s3 1 3 2.5zM7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7z"/></svg> + </a> + </h4> + <p class="mb-2 get-repo-decription-text"> + Use Git or checkout with SVN using the web URL. + </p> + + <div class="input-group"> + <input type="text" class="form-control input-monospace input-sm" data-autoselect value="https://github.com/huster16/gatk-tools.git" aria-label="Clone this repository at https://github.com/huster16/gatk-tools.git" readonly> + <div class="input-group-button"> + <clipboard-copy value="https://github.com/huster16/gatk-tools.git" aria-label="Copy to clipboard" class="btn btn-sm" data-hydro-click="{"event_type":"clone_or_download.click","payload":{"feature_clicked":"COPY_URL","git_repository_type":"REPOSITORY","repository_id":189599350,"client_id":null,"originating_request_id":"9296:3F63:B1FBFC:1321364:5CF25B7F","originating_url":"https://github.com/huster16/gatk-tools","referrer":null,"user_id":null}}" data-hydro-click-hmac="11678c39c42eee5608601cea62776722ddc19e672194910a3f7e339e0c1dd6e6"><svg class="octicon octicon-clippy" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M2 13h4v1H2v-1zm5-6H2v1h5V7zm2 3V8l-3 3 3 3v-2h5v-2H9zM4.5 9H2v1h2.5V9zM2 12h2.5v-1H2v1zm9 1h1v2c-.02.28-.11.52-.3.7-.19.18-.42.28-.7.3H1c-.55 0-1-.45-1-1V4c0-.55.45-1 1-1h3c0-1.11.89-2 2-2 1.11 0 2 .89 2 2h3c.55 0 1 .45 1 1v5h-1V6H1v9h10v-2zM2 5h8c0-.55-.45-1-1-1H8c-.55 0-1-.45-1-1s-.45-1-1-1-1 .45-1 1-.45 1-1 1H3c-.55 0-1 .45-1 1z"/></svg></clipboard-copy> + </div> +</div> + + </div> + + <div class="mt-2"> + +<a class="btn btn-outline get-repo-btn js-anon-download-zip-link " rel="nofollow" data-hydro-click="{"event_type":"clone_or_download.click","payload":{"feature_clicked":"DOWNLOAD_ZIP","git_repository_type":"REPOSITORY","repository_id":189599350,"client_id":null,"originating_request_id":"9296:3F63:B1FBFC:1321364:5CF25B7F","originating_url":"https://github.com/huster16/gatk-tools","referrer":null,"user_id":null}}" data-hydro-click-hmac="f38afae5eed2525a512560364e73cf9629a62f093e6936acc841e643eb1f6dc8" data-ga-click="Repository, download zip, location:repo overview" href="/huster16/gatk-tools/archive/master.zip">Download ZIP</a> + + </div> + </div> + + <div class="js-modal-downloading" hidden> + <div class="py-2 px-3"> + <h4 class="lh-condensed mb-3">Downloading<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4> + <p class="text-gray"> + Want to be 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class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="print_reads.xml" id="084bb1c569888ece53345b6d80b919d7-19269244ac276c5ac4c3ea35d88a0faa1c63dbf1" href="/huster16/gatk-tools/blob/master/print_reads.xml">print_reads.xml</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"></span> + </td> + </tr> + <tr class="js-navigation-item"> + <td class="icon"> + <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg> + <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="realigner_target_creator.xml" id="00d1312b6f84e2192f19921c8e5e53d7-86621b8b4cbbf521fa5741f6fecc16f87c810c1d" href="/huster16/gatk-tools/blob/master/realigner_target_creator.xml">realigner_target_creator.xml</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"></span> + </td> + </tr> + <tr class="js-navigation-item"> + <td class="icon"> + <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg> + <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="tool_data_table_conf.xml.sample" id="60160a6e4efd651b475bcbf960abcc2d-b0e4b46b92ceb44e50c9abf01cf31db95628ac93" href="/huster16/gatk-tools/blob/master/tool_data_table_conf.xml.sample">tool_data_table_conf.xml.sample</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"></span> + </td> + </tr> + <tr class="js-navigation-item"> + <td class="icon"> + <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg> + <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="tool_dependencies.xml" id="1f1e2fcbf1ddc07a88bc59ca246c9a90-3ac9ffc6df38d4633e8022ed0b78e3c95e586b10" href="/huster16/gatk-tools/blob/master/tool_dependencies.xml">tool_dependencies.xml</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"></span> + </td> + </tr> + </tbody> + </table> + +</include-fragment> + + + + <div id="readme" class="Box Box--condensed instapaper_body js-code-block-container"> + <div class="Box-header d-flex flex-items-center flex-justify-between px-2"> + <h3 class="Box-title pr-3"> + <svg class="octicon octicon-book" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M3 5h4v1H3V5zm0 3h4V7H3v1zm0 2h4V9H3v1zm11-5h-4v1h4V5zm0 2h-4v1h4V7zm0 2h-4v1h4V9zm2-6v9c0 .55-.45 1-1 1H9.5l-1 1-1-1H2c-.55 0-1-.45-1-1V3c0-.55.45-1 1-1h5.5l1 1 1-1H15c.55 0 1 .45 1 1zm-8 .5L7.5 3H2v9h6V3.5zm7-.5H9.5l-.5.5V12h6V3z"/></svg> + README + </h3> + </div> + <div class="Box-body"> + <div class="plain"><pre style="white-space: pre-wrap">Installation note: +A GATK license needs to be obtained separately from the Broad Institute (<a href="https://www.broadinstitute.org/gatk/" rel="nofollow">https://www.broadinstitute.org/gatk/</a>) +to be able to use this tool. Once the license is obtained, the GATK Jar file must then be downloaded and moved +to /mnt/galaxy/tools/GATK/x.x-x on the server. Substitute the appropriate version number in the file path. +Be sure to download the correct version of the Jar file for the toolshed version installed. +</pre></div> + </div> + </div> + + + + </div> + <div class="modal-backdrop js-touch-events"></div> +</div> + + </main> + </div> + + + </div> + + +<div class="footer container-lg width-full px-3" role="contentinfo"> + <div class="position-relative d-flex flex-justify-between pt-6 pb-2 mt-6 f6 text-gray border-top border-gray-light "> + <ul class="list-style-none d-flex flex-wrap "> + <li class="mr-3">© 2019 <span title="0.27328s from unicorn-68fcf5fc59-q8f8h">GitHub</span>, Inc.</li> + <li class="mr-3"><a data-ga-click="Footer, go to terms, text:terms" href="https://github.com/site/terms">Terms</a></li> + <li class="mr-3"><a data-ga-click="Footer, go to privacy, text:privacy" href="https://github.com/site/privacy">Privacy</a></li> + <li class="mr-3"><a data-ga-click="Footer, go to security, text:security" 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