Mercurial > repos > scottx611x > qualimap2_bamqc
changeset 30:418ee04dd1b2 draft
planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
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--- a/qualimap_bamqc.py Thu Jul 26 16:21:44 2018 -0400 +++ b/qualimap_bamqc.py Thu Jul 26 16:40:19 2018 -0400 @@ -2,17 +2,18 @@ from __future__ import print_function import argparse from subprocess import check_call, CalledProcessError -import os import shutil import sys +OUTPUT_DIR = "qualimap_results" + def qualimap_bamqc(bam_filename, genomecov_file, jv_mem_size): qualimap_command = [ "qualimap", "bamqc", "-bam " + bam_filename, "-oc " + genomecov_file, - "-outdir .", + "-outdir " + OUTPUT_DIR, "--java-mem-size=" + jv_mem_size ] @@ -38,12 +39,12 @@ args.java_mem_size ) - print(os.listdir("../")) - + shutil.move(OUTPUT_DIR + "/genome_results.txt", "genome_results.txt") + shutil.move(OUTPUT_DIR + "/qualimapReport.html", "qualimapReport.html") shutil.make_archive( 'raw_data_qualimapReport', 'zip', - os.path.join("../", 'raw_data_qualimapReport') + OUTPUT_DIR + '/raw_data_qualimapReport' )
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/css/agogo.css Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,471 @@ +/* + * agogo.css_t + * ~~~~~~~~~~~ + * + * Sphinx stylesheet -- agogo theme. + * + * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +* { + margin: 0px; + padding: 0px; +} + +body { + font-family: "Verdana", Arial, sans-serif; + line-height: 1.4em; + color: black; + background-color: #eeeeec; +} + + +/* Page layout */ + +div.header, div.content, div.footer { + width: 70em; + margin-left: auto; + margin-right: auto; +} + +div.header-wrapper { + background: url(bgtop.png) top left repeat-x; + border-bottom: 3px solid #2e3436; +} + + +/* Default body styles */ +a { + color: #ce5c00; +} + +div.bodywrapper a, div.footer a { + text-decoration: underline; +} + +.clearer { + clear: both; +} + +.left { + float: left; +} + +.right { + float: right; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +h1, h2, h3, h4 { + font-family: "Georgia", "Times New Roman", serif; + font-weight: normal; + color: #3465a4; + margin-bottom: .8em; +} + +h1 { + color: #204a87; +} + +h2 { + padding-bottom: .5em; + border-bottom: 1px solid #3465a4; +} + +a.headerlink { + visibility: hidden; + color: #dddddd; + padding-left: .3em; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink { + visibility: visible; +} + +img { + border: 0; +} + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 2px 7px 1px 7px; + border-left: 0.2em solid black; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +dt:target, .highlighted { + background-color: #fbe54e; +} + +/* Header */ + +div.header { + padding-top: 10px; + padding-bottom: 10px; +} + +div.header .headertitle { + font-family: "Georgia", "Times New Roman", serif; + font-weight: normal; + font-size: 180%; + letter-spacing: .08em; + margin-bottom: .8em; +} + +div.header .headertitle a { + color: white; +} + +div.header div.rel { + margin-top: 1em; +} + +div.header div.rel a { + color: #fcaf3e; + letter-spacing: .1em; + text-transform: uppercase; +} + +p.logo { + float: right; +} + +img.logo { + border: 0; +} + + +/* Content */ +div.content-wrapper { + background-color: white; + padding-top: 20px; + padding-bottom: 20px; +} + +div.document { + width: 50em; + float: left; +} + +div.body { + padding-right: 2em; + text-align: justify; +} + +div.document h1 { + line-height: 120%; +} + +div.document ul { + margin: 1.5em; + list-style-type: square; +} + +div.document dd { + margin-left: 1.2em; + margin-top: .4em; + margin-bottom: 1em; +} + +div.document .section { + margin-top: 1.7em; +} +div.document .section:first-child { + margin-top: 0px; +} + +div.document div.highlight { + padding: 3px; + background-color: #eeeeec; + border-top: 2px solid #dddddd; + border-bottom: 2px solid #dddddd; + margin-top: .8em; + margin-bottom: .8em; +} + +div.document h2 { + margin-top: .7em; +} + +div.document p { + margin-bottom: .5em; +} + +div.document li.toctree-l1 { + margin-bottom: 1em; +} + +div.document .descname { + font-weight: bold; +} + +div.document .docutils.literal { + background-color: #eeeeec; + padding: 1px; +} + +div.document .docutils.xref.literal { + background-color: transparent; + padding: 0px; +} + +div.document blockquote { + margin: 1em; +} + +div.document ol { + margin: 1.5em; +} + + +/* Sidebar */ + +div.sidebar { + width: 20em; + float: right; + font-size: .9em; +} + +div.sidebar a, div.header a { + text-decoration: none; +} + +div.sidebar a:hover, div.header a:hover { + text-decoration: underline; +} + +div.sidebar h3 { + color: #2e3436; + text-transform: uppercase; + font-size: 130%; + letter-spacing: .1em; +} + +div.sidebar ul { + list-style-type: none; +} + +div.sidebar li.toctree-l1 a { + display: block; + padding: 1px; + border: 1px solid #dddddd; + background-color: #eeeeec; + margin-bottom: .4em; + padding-left: 3px; + color: #2e3436; +} + +div.sidebar li.toctree-l2 a { + background-color: transparent; + border: none; + margin-left: 1em; + border-bottom: 1px solid #dddddd; +} + +div.sidebar li.toctree-l3 a { + background-color: transparent; + border: none; + margin-left: 2em; + border-bottom: 1px solid #dddddd; +} + +div.sidebar li.toctree-l2:last-child a { + border-bottom: none; +} + +div.sidebar li.toctree-l1.current a { + border-right: 5px solid #fcaf3e; +} + +div.sidebar li.toctree-l1.current li.toctree-l2 a { + border-right: none; +} + +div.sidebar input[type="text"] { + width: 170px; +} + +div.sidebar input[type="submit"] { + width: 30px; +} + + +/* Footer */ + +div.footer-wrapper { + background: url(bgfooter.png) top left repeat-x; + border-top: 4px solid #babdb6; + padding-top: 10px; + padding-bottom: 10px; + min-height: 80px; +} + +div.footer, div.footer a { + color: #888a85; +} + +div.footer .right { + text-align: right; +} + +div.footer .left { + text-transform: uppercase; +} + + +/* Styles copied from basic theme */ + +img.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-center-qualimap { + display: block; + margin-left: auto; + margin-right: auto; + width: 100% +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li div.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable dl, table.indextable dd { + margin-top: 0; + margin-bottom: 0; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +/* -- viewcode extension ---------------------------------------------------- */ + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family:: "Verdana", Arial, sans-serif; +} + +div.viewcode-block:target { + margin: -1px -3px; + padding: 0 3px; + background-color: #f4debf; + border-top: 1px solid #ac9; + border-bottom: 1px solid #ac9; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/css/basic.css Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,540 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 0px; + margin-left: -100%; + font-size: 90%; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox input[type="text"] { + width: 170px; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + width: 30px; +} + +img { + border: 0; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li div.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable dl, table.indextable dd { + margin-top: 0; + margin-bottom: 0; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- general body styles --------------------------------------------------- */ + +a.headerlink { + visibility: hidden; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.field-list ul { + padding-left: 1em; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px 7px 0 7px; + background-color: #ffe; + width: 40%; + float: right; +} + +p.sidebar-title { + font-weight: bold; +} + +/* -- topics ---------------------------------------------------------------- */ + +div.topic { + border: 1px solid #ccc; + padding: 7px 7px 0 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +div.admonition dl { + margin-bottom: 0; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + border: 0; + border-collapse: collapse; +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +table.field-list td, table.field-list th { + border: 0 !important; +} + +table.footnote td, table.footnote th { + border: 0 !important; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +dl { + margin-bottom: 15px; +} + +dd p { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +dt:target, .highlighted { + background-color: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.refcount { + color: #060; +} + +.optional { + font-size: 1.3em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +td.linenos pre { + padding: 5px 0px; + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + margin-left: 0.5em; +} + +table.highlighttable td { + padding: 0 0.5em 0 0.5em; +} + +tt.descname { + background-color: transparent; + font-weight: bold; + font-size: 1.2em; +} + +tt.descclassname { + background-color: transparent; +} + +tt.xref, a tt { + background-color: transparent; + font-weight: bold; +} + +h1 tt, h2 tt, h3 tt, h4 tt, h5 tt, h6 tt { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/css/doctools.js Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,247 @@ +/* + * doctools.js + * ~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for all documentation. + * + * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/** + * select a different prefix for underscore + */ +$u = _.noConflict(); + +/** + * make the code below compatible with browsers without + * an installed firebug like debugger +if (!window.console || !console.firebug) { + var names = ["log", "debug", "info", "warn", "error", "assert", "dir", + "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace", + "profile", "profileEnd"]; + window.console = {}; + for (var i = 0; i < names.length; ++i) + window.console[names[i]] = function() {}; +} + */ + +/** + * small helper function to urldecode strings + */ +jQuery.urldecode = function(x) { + return decodeURIComponent(x).replace(/\+/g, ' '); +} + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s == 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * small function to check if an array contains + * a given item. + */ +jQuery.contains = function(arr, item) { + for (var i = 0; i < arr.length; i++) { + if (arr[i] == item) + return true; + } + return false; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node) { + if (node.nodeType == 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) { + var span = document.createElement("span"); + span.className = className; + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this); + }); + } + } + return this.each(function() { + highlight(this); + }); +}; + +/** + * Small JavaScript module for the documentation. + */ +var Documentation = { + + init : function() { + this.fixFirefoxAnchorBug(); + this.highlightSearchWords(); + this.initIndexTable(); + }, + + /** + * i18n support + */ + TRANSLATIONS : {}, + PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; }, + LOCALE : 'unknown', + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext : function(string) { + var translated = Documentation.TRANSLATIONS[string]; + if (typeof translated == 'undefined') + return string; + return (typeof translated == 'string') ? translated : translated[0]; + }, + + ngettext : function(singular, plural, n) { + var translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated == 'undefined') + return (n == 1) ? singular : plural; + return translated[Documentation.PLURALEXPR(n)]; + }, + + addTranslations : function(catalog) { + for (var key in catalog.messages) + this.TRANSLATIONS[key] = catalog.messages[key]; + this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')'); + this.LOCALE = catalog.locale; + }, + + /** + * add context elements like header anchor links + */ + addContextElements : function() { + $('div[id] > :header:first').each(function() { + $('<a class="headerlink">\u00B6</a>'). + attr('href', '#' + this.id). + attr('title', _('Permalink to this headline')). + appendTo(this); + }); + $('dt[id]').each(function() { + $('<a class="headerlink">\u00B6</a>'). + attr('href', '#' + this.id). + attr('title', _('Permalink to this definition')). + appendTo(this); + }); + }, + + /** + * workaround a firefox stupidity + */ + fixFirefoxAnchorBug : function() { + if (document.location.hash && $.browser.mozilla) + window.setTimeout(function() { + document.location.href += ''; + }, 10); + }, + + /** + * highlight the search words provided in the url in the text + */ + highlightSearchWords : function() { + var params = $.getQueryParameters(); + var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : []; + if (terms.length) { + var body = $('div.body'); + window.setTimeout(function() { + $.each(terms, function() { + body.highlightText(this.toLowerCase(), 'highlighted'); + }); + }, 10); + $('<p class="highlight-link"><a href="javascript:Documentation.' + + 'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>') + .appendTo($('#searchbox')); + } + }, + + /** + * init the domain index toggle buttons + */ + initIndexTable : function() { + var togglers = $('img.toggler').click(function() { + var src = $(this).attr('src'); + var idnum = $(this).attr('id').substr(7); + $('tr.cg-' + idnum).toggle(); + if (src.substr(-9) == 'minus.png') + $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); + else + $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); + }).css('display', ''); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) { + togglers.click(); + } + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords : function() { + $('#searchbox .highlight-link').fadeOut(300); + $('span.highlighted').removeClass('highlighted'); + }, + + /** + * make the url absolute + */ + makeURL : function(relativeURL) { + return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL; + }, + + /** + * get the current relative url + */ + getCurrentURL : function() { + var path = document.location.pathname; + var parts = path.split(/\//); + $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() { + if (this == '..') + parts.pop(); + }); + var url = parts.join('/'); + return path.substring(url.lastIndexOf('/') + 1, path.length - 1); + } +}; + +// quick alias for translations +_ = Documentation.gettext; + +$(document).ready(function() { + Documentation.init(); +});
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/css/pygments.css Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,62 @@ +.highlight .hll { background-color: #ffffcc } +.highlight { background: #eeffcc; } +.highlight .c { color: #408090; font-style: italic } /* Comment */ +.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .k { color: #007020; font-weight: bold } /* Keyword */ +.highlight .o { color: #666666 } /* Operator */ +.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #007020 } /* Comment.Preproc */ +.highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */ +.highlight .gd { color: #A00000 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ +.highlight .gr { color: #FF0000 } /* Generic.Error */ +.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */ +.highlight .gi { color: #00A000 } /* Generic.Inserted */ +.highlight .go { color: #303030 } /* Generic.Output */ +.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */ +.highlight .gs { font-weight: bold } /* Generic.Strong */ +.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */ +.highlight .gt { color: #0040D0 } /* Generic.Traceback */ +.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */ +.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */ +.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */ +.highlight .kp { color: #007020 } /* Keyword.Pseudo */ +.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */ +.highlight .kt { color: #902000 } /* Keyword.Type */ +.highlight .m { color: #208050 } /* Literal.Number */ +.highlight .s { color: #4070a0 } /* Literal.String */ +.highlight .na { color: #4070a0 } /* Name.Attribute */ +.highlight .nb { color: #007020 } /* Name.Builtin */ +.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */ +.highlight .no { color: #60add5 } /* Name.Constant */ +.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */ +.highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */ +.highlight .ne { color: #007020 } /* Name.Exception */ +.highlight .nf { color: #06287e } /* Name.Function */ +.highlight .nl { color: #002070; font-weight: bold } /* Name.Label */ +.highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */ +.highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */ +.highlight .nv { color: #bb60d5 } /* Name.Variable */ +.highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */ +.highlight .w { color: #bbbbbb } /* Text.Whitespace */ +.highlight .mf { color: #208050 } /* Literal.Number.Float */ +.highlight .mh { color: #208050 } /* Literal.Number.Hex */ +.highlight .mi { color: #208050 } /* Literal.Number.Integer */ +.highlight .mo { color: #208050 } /* Literal.Number.Oct */ +.highlight .sb { color: #4070a0 } /* Literal.String.Backtick */ +.highlight .sc { color: #4070a0 } /* Literal.String.Char */ +.highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */ +.highlight .s2 { color: #4070a0 } /* Literal.String.Double */ +.highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */ +.highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */ +.highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */ +.highlight .sx { color: #c65d09 } /* Literal.String.Other */ +.highlight .sr { color: #235388 } /* Literal.String.Regex */ +.highlight .s1 { color: #4070a0 } /* Literal.String.Single */ +.highlight .ss { color: #517918 } /* Literal.String.Symbol */ +.highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */ +.highlight .vc { color: #bb60d5 } /* Name.Variable.Class */ +.highlight .vg { color: #bb60d5 } /* Name.Variable.Global */ +.highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */ +.highlight .il { color: #208050 } /* Literal.Number.Integer.Long */ \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/css/report.css Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,50 @@ +div.summary{ + +} + +table.summary{ + + border: 0px; + width: 100%; + vertical-align: top; + +} + +div.table-summary{ + margin-left:auto; + margin-right:auto; + padding-bottom: 20px; +} + +td.column1{ + width: 60%; +} + +table.hovertable { + + font-size:14px; + + border-width: 1px; + border-color: #999999; + border-collapse: collapse; +} +table.hovertable th { + background-color:#FFFFFF; + border-width: 1px; + padding: 8px; + border-style: solid; + border-color: #a9c6c9; +} +table.hovertable tr { + background-color:#FFFFFF; +} +table.hovertable td { + border-width: 1px; + padding: 8px; + border-style: solid; + border-color: #a9c6c9; +} + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/css/searchtools.js Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,560 @@ +/* + * searchtools.js_t + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilties for the full-text search. + * + * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words, hlwords is the list of normal, unstemmed + * words. the first one is used to find the occurance, the + * latter for highlighting it. + */ + +jQuery.makeSearchSummary = function(text, keywords, hlwords) { + var textLower = text.toLowerCase(); + var start = 0; + $.each(keywords, function() { + var i = textLower.indexOf(this.toLowerCase()); + if (i > -1) + start = i; + }); + start = Math.max(start - 120, 0); + var excerpt = ((start > 0) ? '...' : '') + + $.trim(text.substr(start, 240)) + + ((start + 240 - text.length) ? '...' : ''); + var rv = $('<div class="context"></div>').text(excerpt); + $.each(hlwords, function() { + rv = rv.highlightText(this, 'highlighted'); + }); + return rv; +} + + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + + +/** + * Search Module + */ +var Search = { + + _index : null, + _queued_query : null, + _pulse_status : -1, + + init : function() { + var params = $.getQueryParameters(); + if (params.q) { + var query = params.q[0]; + $('input[name="q"]')[0].value = query; + this.performSearch(query); + } + }, + + loadIndex : function(url) { + $.ajax({type: "GET", url: url, data: null, success: null, + dataType: "script", cache: true}); + }, + + setIndex : function(index) { + var q; + this._index = index; + if ((q = this._queued_query) !== null) { + this._queued_query = null; + Search.query(q); + } + }, + + hasIndex : function() { + return this._index !== null; + }, + + deferQuery : function(query) { + this._queued_query = query; + }, + + stopPulse : function() { + this._pulse_status = 0; + }, + + startPulse : function() { + if (this._pulse_status >= 0) + return; + function pulse() { + Search._pulse_status = (Search._pulse_status + 1) % 4; + var dotString = ''; + for (var i = 0; i < Search._pulse_status; i++) + dotString += '.'; + Search.dots.text(dotString); + if (Search._pulse_status > -1) + window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something + */ + performSearch : function(query) { + // create the required interface elements + this.out = $('#search-results'); + this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out); + this.dots = $('<span></span>').appendTo(this.title); + this.status = $('<p style="display: none"></p>').appendTo(this.out); + this.output = $('<ul class="search"/>').appendTo(this.out); + + $('#search-progress').text(_('Preparing search...')); + this.startPulse(); + + // index already loaded, the browser was quick! + if (this.hasIndex()) + this.query(query); + else + this.deferQuery(query); + }, + + query : function(query) { + var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"]; + + // Stem the searchterms and add them to the correct list + var stemmer = new Stemmer(); + var searchterms = []; + var excluded = []; + var hlterms = []; + var tmp = query.split(/\s+/); + var objectterms = []; + for (var i = 0; i < tmp.length; i++) { + if (tmp[i] != "") { + objectterms.push(tmp[i].toLowerCase()); + } + + if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) || + tmp[i] == "") { + // skip this "word" + continue; + } + // stem the word + var word = stemmer.stemWord(tmp[i]).toLowerCase(); + // select the correct list + if (word[0] == '-') { + var toAppend = excluded; + word = word.substr(1); + } + else { + var toAppend = searchterms; + hlterms.push(tmp[i].toLowerCase()); + } + // only add if not already in the list + if (!$.contains(toAppend, word)) + toAppend.push(word); + }; + var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" ")); + + // console.debug('SEARCH: searching for:'); + // console.info('required: ', searchterms); + // console.info('excluded: ', excluded); + + // prepare search + var filenames = this._index.filenames; + var titles = this._index.titles; + var terms = this._index.terms; + var fileMap = {}; + var files = null; + // different result priorities + var importantResults = []; + var objectResults = []; + var regularResults = []; + var unimportantResults = []; + $('#search-progress').empty(); + + // lookup as object + for (var i = 0; i < objectterms.length; i++) { + var others = [].concat(objectterms.slice(0,i), + objectterms.slice(i+1, objectterms.length)) + var results = this.performObjectSearch(objectterms[i], others); + // Assume first word is most likely to be the object, + // other words more likely to be in description. + // Therefore put matches for earlier words first. + // (Results are eventually used in reverse order). + objectResults = results[0].concat(objectResults); + importantResults = results[1].concat(importantResults); + unimportantResults = results[2].concat(unimportantResults); + } + + // perform the search on the required terms + for (var i = 0; i < searchterms.length; i++) { + var word = searchterms[i]; + // no match but word was a required one + if ((files = terms[word]) == null) + break; + if (files.length == undefined) { + files = [files]; + } + // create the mapping + for (var j = 0; j < files.length; j++) { + var file = files[j]; + if (file in fileMap) + fileMap[file].push(word); + else + fileMap[file] = [word]; + } + } + + // now check if the files don't contain excluded terms + for (var file in fileMap) { + var valid = true; + + // check if all requirements are matched + if (fileMap[file].length != searchterms.length) + continue; + + // ensure that none of the excluded terms is in the + // search result. + for (var i = 0; i < excluded.length; i++) { + if (terms[excluded[i]] == file || + $.contains(terms[excluded[i]] || [], file)) { + valid = false; + break; + } + } + + // if we have still a valid result we can add it + // to the result list + if (valid) + regularResults.push([filenames[file], titles[file], '', null]); + } + + // delete unused variables in order to not waste + // memory until list is retrieved completely + delete filenames, titles, terms; + + // now sort the regular results descending by title + regularResults.sort(function(a, b) { + var left = a[1].toLowerCase(); + var right = b[1].toLowerCase(); + return (left > right) ? -1 : ((left < right) ? 1 : 0); + }); + + // combine all results + var results = unimportantResults.concat(regularResults) + .concat(objectResults).concat(importantResults); + + // print the results + var resultCount = results.length; + function displayNextItem() { + // results left, load the summary and display it + if (results.length) { + var item = results.pop(); + var listItem = $('<li style="display:none"></li>'); + if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') { + // dirhtml builder + var dirname = item[0] + '/'; + if (dirname.match(/\/index\/$/)) { + dirname = dirname.substring(0, dirname.length-6); + } else if (dirname == 'index/') { + dirname = ''; + } + listItem.append($('<a/>').attr('href', + DOCUMENTATION_OPTIONS.URL_ROOT + dirname + + highlightstring + item[2]).html(item[1])); + } else { + // normal html builders + listItem.append($('<a/>').attr('href', + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX + + highlightstring + item[2]).html(item[1])); + } + if (item[3]) { + listItem.append($('<span> (' + item[3] + ')</span>')); + Search.output.append(listItem); + listItem.slideDown(5, function() { + displayNextItem(); + }); + } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) { + $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + + item[0] + '.txt', function(data) { + if (data != '') { + listItem.append($.makeSearchSummary(data, searchterms, hlterms)); + Search.output.append(listItem); + } + listItem.slideDown(5, function() { + displayNextItem(); + }); + }, "text"); + } else { + // no source available, just display title + Search.output.append(listItem); + listItem.slideDown(5, function() { + displayNextItem(); + }); + } + } + // search finished, update title and status message + else { + Search.stopPulse(); + Search.title.text(_('Search Results')); + if (!resultCount) + Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.')); + else + Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount)); + Search.status.fadeIn(500); + } + } + displayNextItem(); + }, + + performObjectSearch : function(object, otherterms) { + var filenames = this._index.filenames; + var objects = this._index.objects; + var objnames = this._index.objnames; + var titles = this._index.titles; + + var importantResults = []; + var objectResults = []; + var unimportantResults = []; + + for (var prefix in objects) { + for (var name in objects[prefix]) { + var fullname = (prefix ? prefix + '.' : '') + name; + if (fullname.toLowerCase().indexOf(object) > -1) { + var match = objects[prefix][name]; + var objname = objnames[match[1]][2]; + var title = titles[match[0]]; + // If more than one term searched for, we require other words to be + // found in the name/title/description + if (otherterms.length > 0) { + var haystack = (prefix + ' ' + name + ' ' + + objname + ' ' + title).toLowerCase(); + var allfound = true; + for (var i = 0; i < otherterms.length; i++) { + if (haystack.indexOf(otherterms[i]) == -1) { + allfound = false; + break; + } + } + if (!allfound) { + continue; + } + } + var descr = objname + _(', in ') + title; + anchor = match[3]; + if (anchor == '') + anchor = fullname; + else if (anchor == '-') + anchor = objnames[match[1]][1] + '-' + fullname; + result = [filenames[match[0]], fullname, '#'+anchor, descr]; + switch (match[2]) { + case 1: objectResults.push(result); break; + case 0: importantResults.push(result); break; + case 2: unimportantResults.push(result); break; + } + } + } + } + + // sort results descending + objectResults.sort(function(a, b) { + return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0); + }); + + importantResults.sort(function(a, b) { + return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0); + }); + + unimportantResults.sort(function(a, b) { + return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0); + }); + + return [importantResults, objectResults, unimportantResults] + } +} + +$(document).ready(function() { + Search.init(); +}); \ No newline at end of file
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/css/websupport.js Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,808 @@ +/* + * websupport.js + * ~~~~~~~~~~~~~ + * + * sphinx.websupport utilties for all documentation. + * + * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +(function($) { + $.fn.autogrow = function() { + return this.each(function() { + var textarea = this; + + $.fn.autogrow.resize(textarea); + + $(textarea) + .focus(function() { + textarea.interval = setInterval(function() { + $.fn.autogrow.resize(textarea); + }, 500); + }) + .blur(function() { + clearInterval(textarea.interval); + }); + }); + }; + + $.fn.autogrow.resize = function(textarea) { + var lineHeight = parseInt($(textarea).css('line-height'), 10); + var lines = textarea.value.split('\n'); + var columns = textarea.cols; + var lineCount = 0; + $.each(lines, function() { + lineCount += Math.ceil(this.length / columns) || 1; + }); + var height = lineHeight * (lineCount + 1); + $(textarea).css('height', height); + }; +})(jQuery); + +(function($) { + var comp, by; + + function init() { + initEvents(); + initComparator(); + } + + function initEvents() { + $('a.comment-close').live("click", function(event) { + event.preventDefault(); + hide($(this).attr('id').substring(2)); + }); + $('a.vote').live("click", function(event) { + event.preventDefault(); + handleVote($(this)); + }); + $('a.reply').live("click", function(event) { + event.preventDefault(); + openReply($(this).attr('id').substring(2)); + }); + $('a.close-reply').live("click", function(event) { + event.preventDefault(); + closeReply($(this).attr('id').substring(2)); + }); + $('a.sort-option').live("click", function(event) { + event.preventDefault(); + handleReSort($(this)); + }); + $('a.show-proposal').live("click", function(event) { + event.preventDefault(); + showProposal($(this).attr('id').substring(2)); + }); + $('a.hide-proposal').live("click", function(event) { + event.preventDefault(); + hideProposal($(this).attr('id').substring(2)); + }); + $('a.show-propose-change').live("click", function(event) { + event.preventDefault(); + showProposeChange($(this).attr('id').substring(2)); + }); + $('a.hide-propose-change').live("click", function(event) { + event.preventDefault(); + hideProposeChange($(this).attr('id').substring(2)); + }); + $('a.accept-comment').live("click", function(event) { + event.preventDefault(); + acceptComment($(this).attr('id').substring(2)); + }); + $('a.delete-comment').live("click", function(event) { + event.preventDefault(); + deleteComment($(this).attr('id').substring(2)); + }); + $('a.comment-markup').live("click", function(event) { + event.preventDefault(); + toggleCommentMarkupBox($(this).attr('id').substring(2)); + }); + } + + /** + * Set comp, which is a comparator function used for sorting and + * inserting comments into the list. + */ + function setComparator() { + // If the first three letters are "asc", sort in ascending order + // and remove the prefix. + if (by.substring(0,3) == 'asc') { + var i = by.substring(3); + comp = function(a, b) { return a[i] - b[i]; }; + } else { + // Otherwise sort in descending order. + comp = function(a, b) { return b[by] - a[by]; }; + } + + // Reset link styles and format the selected sort option. + $('a.sel').attr('href', '#').removeClass('sel'); + $('a.by' + by).removeAttr('href').addClass('sel'); + } + + /** + * Create a comp function. If the user has preferences stored in + * the sortBy cookie, use those, otherwise use the default. + */ + function initComparator() { + by = 'rating'; // Default to sort by rating. + // If the sortBy cookie is set, use that instead. + if (document.cookie.length > 0) { + var start = document.cookie.indexOf('sortBy='); + if (start != -1) { + start = start + 7; + var end = document.cookie.indexOf(";", start); + if (end == -1) { + end = document.cookie.length; + by = unescape(document.cookie.substring(start, end)); + } + } + } + setComparator(); + } + + /** + * Show a comment div. + */ + function show(id) { + $('#ao' + id).hide(); + $('#ah' + id).show(); + var context = $.extend({id: id}, opts); + var popup = $(renderTemplate(popupTemplate, context)).hide(); + popup.find('textarea[name="proposal"]').hide(); + popup.find('a.by' + by).addClass('sel'); + var form = popup.find('#cf' + id); + form.submit(function(event) { + event.preventDefault(); + addComment(form); + }); + $('#s' + id).after(popup); + popup.slideDown('fast', function() { + getComments(id); + }); + } + + /** + * Hide a comment div. + */ + function hide(id) { + $('#ah' + id).hide(); + $('#ao' + id).show(); + var div = $('#sc' + id); + div.slideUp('fast', function() { + div.remove(); + }); + } + + /** + * Perform an ajax request to get comments for a node + * and insert the comments into the comments tree. + */ + function getComments(id) { + $.ajax({ + type: 'GET', + url: opts.getCommentsURL, + data: {node: id}, + success: function(data, textStatus, request) { + var ul = $('#cl' + id); + var speed = 100; + $('#cf' + id) + .find('textarea[name="proposal"]') + .data('source', data.source); + + if (data.comments.length === 0) { + ul.html('<li>No comments yet.</li>'); + ul.data('empty', true); + } else { + // If there are comments, sort them and put them in the list. + var comments = sortComments(data.comments); + speed = data.comments.length * 100; + appendComments(comments, ul); + ul.data('empty', false); + } + $('#cn' + id).slideUp(speed + 200); + ul.slideDown(speed); + }, + error: function(request, textStatus, error) { + showError('Oops, there was a problem retrieving the comments.'); + }, + dataType: 'json' + }); + } + + /** + * Add a comment via ajax and insert the comment into the comment tree. + */ + function addComment(form) { + var node_id = form.find('input[name="node"]').val(); + var parent_id = form.find('input[name="parent"]').val(); + var text = form.find('textarea[name="comment"]').val(); + var proposal = form.find('textarea[name="proposal"]').val(); + + if (text == '') { + showError('Please enter a comment.'); + return; + } + + // Disable the form that is being submitted. + form.find('textarea,input').attr('disabled', 'disabled'); + + // Send the comment to the server. + $.ajax({ + type: "POST", + url: opts.addCommentURL, + dataType: 'json', + data: { + node: node_id, + parent: parent_id, + text: text, + proposal: proposal + }, + success: function(data, textStatus, error) { + // Reset the form. + if (node_id) { + hideProposeChange(node_id); + } + form.find('textarea') + .val('') + .add(form.find('input')) + .removeAttr('disabled'); + var ul = $('#cl' + (node_id || parent_id)); + if (ul.data('empty')) { + $(ul).empty(); + ul.data('empty', false); + } + insertComment(data.comment); + var ao = $('#ao' + node_id); + ao.find('img').attr({'src': opts.commentBrightImage}); + if (node_id) { + // if this was a "root" comment, remove the commenting box + // (the user can get it back by reopening the comment popup) + $('#ca' + node_id).slideUp(); + } + }, + error: function(request, textStatus, error) { + form.find('textarea,input').removeAttr('disabled'); + showError('Oops, there was a problem adding the comment.'); + } + }); + } + + /** + * Recursively append comments to the main comment list and children + * lists, creating the comment tree. + */ + function appendComments(comments, ul) { + $.each(comments, function() { + var div = createCommentDiv(this); + ul.append($(document.createElement('li')).html(div)); + appendComments(this.children, div.find('ul.comment-children')); + // To avoid stagnating data, don't store the comments children in data. + this.children = null; + div.data('comment', this); + }); + } + + /** + * After adding a new comment, it must be inserted in the correct + * location in the comment tree. + */ + function insertComment(comment) { + var div = createCommentDiv(comment); + + // To avoid stagnating data, don't store the comments children in data. + comment.children = null; + div.data('comment', comment); + + var ul = $('#cl' + (comment.node || comment.parent)); + var siblings = getChildren(ul); + + var li = $(document.createElement('li')); + li.hide(); + + // Determine where in the parents children list to insert this comment. + for(i=0; i < siblings.length; i++) { + if (comp(comment, siblings[i]) <= 0) { + $('#cd' + siblings[i].id) + .parent() + .before(li.html(div)); + li.slideDown('fast'); + return; + } + } + + // If we get here, this comment rates lower than all the others, + // or it is the only comment in the list. + ul.append(li.html(div)); + li.slideDown('fast'); + } + + function acceptComment(id) { + $.ajax({ + type: 'POST', + url: opts.acceptCommentURL, + data: {id: id}, + success: function(data, textStatus, request) { + $('#cm' + id).fadeOut('fast'); + $('#cd' + id).removeClass('moderate'); + }, + error: function(request, textStatus, error) { + showError('Oops, there was a problem accepting the comment.'); + } + }); + } + + function deleteComment(id) { + $.ajax({ + type: 'POST', + url: opts.deleteCommentURL, + data: {id: id}, + success: function(data, textStatus, request) { + var div = $('#cd' + id); + if (data == 'delete') { + // Moderator mode: remove the comment and all children immediately + div.slideUp('fast', function() { + div.remove(); + }); + return; + } + // User mode: only mark the comment as deleted + div + .find('span.user-id:first') + .text('[deleted]').end() + .find('div.comment-text:first') + .text('[deleted]').end() + .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id + + ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id) + .remove(); + var comment = div.data('comment'); + comment.username = '[deleted]'; + comment.text = '[deleted]'; + div.data('comment', comment); + }, + error: function(request, textStatus, error) { + showError('Oops, there was a problem deleting the comment.'); + } + }); + } + + function showProposal(id) { + $('#sp' + id).hide(); + $('#hp' + id).show(); + $('#pr' + id).slideDown('fast'); + } + + function hideProposal(id) { + $('#hp' + id).hide(); + $('#sp' + id).show(); + $('#pr' + id).slideUp('fast'); + } + + function showProposeChange(id) { + $('#pc' + id).hide(); + $('#hc' + id).show(); + var textarea = $('#pt' + id); + textarea.val(textarea.data('source')); + $.fn.autogrow.resize(textarea[0]); + textarea.slideDown('fast'); + } + + function hideProposeChange(id) { + $('#hc' + id).hide(); + $('#pc' + id).show(); + var textarea = $('#pt' + id); + textarea.val('').removeAttr('disabled'); + textarea.slideUp('fast'); + } + + function toggleCommentMarkupBox(id) { + $('#mb' + id).toggle(); + } + + /** Handle when the user clicks on a sort by link. */ + function handleReSort(link) { + var classes = link.attr('class').split(/\s+/); + for (var i=0; i<classes.length; i++) { + if (classes[i] != 'sort-option') { + by = classes[i].substring(2); + } + } + setComparator(); + // Save/update the sortBy cookie. + var expiration = new Date(); + expiration.setDate(expiration.getDate() + 365); + document.cookie= 'sortBy=' + escape(by) + + ';expires=' + expiration.toUTCString(); + $('ul.comment-ul').each(function(index, ul) { + var comments = getChildren($(ul), true); + comments = sortComments(comments); + appendComments(comments, $(ul).empty()); + }); + } + + /** + * Function to process a vote when a user clicks an arrow. + */ + function handleVote(link) { + if (!opts.voting) { + showError("You'll need to login to vote."); + return; + } + + var id = link.attr('id'); + if (!id) { + // Didn't click on one of the voting arrows. + return; + } + // If it is an unvote, the new vote value is 0, + // Otherwise it's 1 for an upvote, or -1 for a downvote. + var value = 0; + if (id.charAt(1) != 'u') { + value = id.charAt(0) == 'u' ? 1 : -1; + } + // The data to be sent to the server. + var d = { + comment_id: id.substring(2), + value: value + }; + + // Swap the vote and unvote links. + link.hide(); + $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id) + .show(); + + // The div the comment is displayed in. + var div = $('div#cd' + d.comment_id); + var data = div.data('comment'); + + // If this is not an unvote, and the other vote arrow has + // already been pressed, unpress it. + if ((d.value !== 0) && (data.vote === d.value * -1)) { + $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide(); + $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show(); + } + + // Update the comments rating in the local data. + data.rating += (data.vote === 0) ? d.value : (d.value - data.vote); + data.vote = d.value; + div.data('comment', data); + + // Change the rating text. + div.find('.rating:first') + .text(data.rating + ' point' + (data.rating == 1 ? '' : 's')); + + // Send the vote information to the server. + $.ajax({ + type: "POST", + url: opts.processVoteURL, + data: d, + error: function(request, textStatus, error) { + showError('Oops, there was a problem casting that vote.'); + } + }); + } + + /** + * Open a reply form used to reply to an existing comment. + */ + function openReply(id) { + // Swap out the reply link for the hide link + $('#rl' + id).hide(); + $('#cr' + id).show(); + + // Add the reply li to the children ul. + var div = $(renderTemplate(replyTemplate, {id: id})).hide(); + $('#cl' + id) + .prepend(div) + // Setup the submit handler for the reply form. + .find('#rf' + id) + .submit(function(event) { + event.preventDefault(); + addComment($('#rf' + id)); + closeReply(id); + }) + .find('input[type=button]') + .click(function() { + closeReply(id); + }); + div.slideDown('fast', function() { + $('#rf' + id).find('textarea').focus(); + }); + } + + /** + * Close the reply form opened with openReply. + */ + function closeReply(id) { + // Remove the reply div from the DOM. + $('#rd' + id).slideUp('fast', function() { + $(this).remove(); + }); + + // Swap out the hide link for the reply link + $('#cr' + id).hide(); + $('#rl' + id).show(); + } + + /** + * Recursively sort a tree of comments using the comp comparator. + */ + function sortComments(comments) { + comments.sort(comp); + $.each(comments, function() { + this.children = sortComments(this.children); + }); + return comments; + } + + /** + * Get the children comments from a ul. If recursive is true, + * recursively include childrens' children. + */ + function getChildren(ul, recursive) { + var children = []; + ul.children().children("[id^='cd']") + .each(function() { + var comment = $(this).data('comment'); + if (recursive) + comment.children = getChildren($(this).find('#cl' + comment.id), true); + children.push(comment); + }); + return children; + } + + /** Create a div to display a comment in. */ + function createCommentDiv(comment) { + if (!comment.displayed && !opts.moderator) { + return $('<div class="moderate">Thank you! Your comment will show up ' + + 'once it is has been approved by a moderator.</div>'); + } + // Prettify the comment rating. + comment.pretty_rating = comment.rating + ' point' + + (comment.rating == 1 ? '' : 's'); + // Make a class (for displaying not yet moderated comments differently) + comment.css_class = comment.displayed ? '' : ' moderate'; + // Create a div for this comment. + var context = $.extend({}, opts, comment); + var div = $(renderTemplate(commentTemplate, context)); + + // If the user has voted on this comment, highlight the correct arrow. + if (comment.vote) { + var direction = (comment.vote == 1) ? 'u' : 'd'; + div.find('#' + direction + 'v' + comment.id).hide(); + div.find('#' + direction + 'u' + comment.id).show(); + } + + if (opts.moderator || comment.text != '[deleted]') { + div.find('a.reply').show(); + if (comment.proposal_diff) + div.find('#sp' + comment.id).show(); + if (opts.moderator && !comment.displayed) + div.find('#cm' + comment.id).show(); + if (opts.moderator || (opts.username == comment.username)) + div.find('#dc' + comment.id).show(); + } + return div; + } + + /** + * A simple template renderer. Placeholders such as <%id%> are replaced + * by context['id'] with items being escaped. Placeholders such as <#id#> + * are not escaped. + */ + function renderTemplate(template, context) { + var esc = $(document.createElement('div')); + + function handle(ph, escape) { + var cur = context; + $.each(ph.split('.'), function() { + cur = cur[this]; + }); + return escape ? esc.text(cur || "").html() : cur; + } + + return template.replace(/<([%#])([\w\.]*)\1>/g, function() { + return handle(arguments[2], arguments[1] == '%' ? true : false); + }); + } + + /** Flash an error message briefly. */ + function showError(message) { + $(document.createElement('div')).attr({'class': 'popup-error'}) + .append($(document.createElement('div')) + .attr({'class': 'error-message'}).text(message)) + .appendTo('body') + .fadeIn("slow") + .delay(2000) + .fadeOut("slow"); + } + + /** Add a link the user uses to open the comments popup. */ + $.fn.comment = function() { + return this.each(function() { + var id = $(this).attr('id').substring(1); + var count = COMMENT_METADATA[id]; + var title = count + ' comment' + (count == 1 ? '' : 's'); + var image = count > 0 ? opts.commentBrightImage : opts.commentImage; + var addcls = count == 0 ? ' nocomment' : ''; + $(this) + .append( + $(document.createElement('a')).attr({ + href: '#', + 'class': 'sphinx-comment-open' + addcls, + id: 'ao' + id + }) + .append($(document.createElement('img')).attr({ + src: image, + alt: 'comment', + title: title + })) + .click(function(event) { + event.preventDefault(); + show($(this).attr('id').substring(2)); + }) + ) + .append( + $(document.createElement('a')).attr({ + href: '#', + 'class': 'sphinx-comment-close hidden', + id: 'ah' + id + }) + .append($(document.createElement('img')).attr({ + src: opts.closeCommentImage, + alt: 'close', + title: 'close' + })) + .click(function(event) { + event.preventDefault(); + hide($(this).attr('id').substring(2)); + }) + ); + }); + }; + + var opts = { + processVoteURL: '/_process_vote', + addCommentURL: '/_add_comment', + getCommentsURL: '/_get_comments', + acceptCommentURL: '/_accept_comment', + deleteCommentURL: '/_delete_comment', + commentImage: '/static/_static/comment.png', + closeCommentImage: '/static/_static/comment-close.png', + loadingImage: '/static/_static/ajax-loader.gif', + commentBrightImage: '/static/_static/comment-bright.png', + upArrow: '/static/_static/up.png', + downArrow: '/static/_static/down.png', + upArrowPressed: '/static/_static/up-pressed.png', + downArrowPressed: '/static/_static/down-pressed.png', + voting: false, + moderator: false + }; + + if (typeof COMMENT_OPTIONS != "undefined") { + opts = jQuery.extend(opts, COMMENT_OPTIONS); + } + + var popupTemplate = '\ + <div class="sphinx-comments" id="sc<%id%>">\ + <p class="sort-options">\ + Sort by:\ + <a href="#" class="sort-option byrating">best rated</a>\ + <a href="#" class="sort-option byascage">newest</a>\ + <a href="#" class="sort-option byage">oldest</a>\ + </p>\ + <div class="comment-header">Comments</div>\ + <div class="comment-loading" id="cn<%id%>">\ + loading comments... <img src="<%loadingImage%>" alt="" /></div>\ + <ul id="cl<%id%>" class="comment-ul"></ul>\ + <div id="ca<%id%>">\ + <p class="add-a-comment">Add a comment\ + (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\ + <div class="comment-markup-box" id="mb<%id%>">\ + reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \ + <tt>``code``</tt>, \ + code blocks: <tt>::</tt> and an indented block after blank line</div>\ + <form method="post" id="cf<%id%>" class="comment-form" action="">\ + <textarea name="comment" cols="80"></textarea>\ + <p class="propose-button">\ + <a href="#" id="pc<%id%>" class="show-propose-change">\ + Propose a change ▹\ + </a>\ + <a href="#" id="hc<%id%>" class="hide-propose-change">\ + Propose a change ▿\ + </a>\ + </p>\ + <textarea name="proposal" id="pt<%id%>" cols="80"\ + spellcheck="false"></textarea>\ + <input type="submit" value="Add comment" />\ + <input type="hidden" name="node" value="<%id%>" />\ + <input type="hidden" name="parent" value="" />\ + </form>\ + </div>\ + </div>'; + + var commentTemplate = '\ + <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\ + <div class="vote">\ + <div class="arrow">\ + <a href="#" id="uv<%id%>" class="vote" title="vote up">\ + <img src="<%upArrow%>" />\ + </a>\ + <a href="#" id="uu<%id%>" class="un vote" title="vote up">\ + <img src="<%upArrowPressed%>" />\ + </a>\ + </div>\ + <div class="arrow">\ + <a href="#" id="dv<%id%>" class="vote" title="vote down">\ + <img src="<%downArrow%>" id="da<%id%>" />\ + </a>\ + <a href="#" id="du<%id%>" class="un vote" title="vote down">\ + <img src="<%downArrowPressed%>" />\ + </a>\ + </div>\ + </div>\ + <div class="comment-content">\ + <p class="tagline comment">\ + <span class="user-id"><%username%></span>\ + <span class="rating"><%pretty_rating%></span>\ + <span class="delta"><%time.delta%></span>\ + </p>\ + <div class="comment-text comment"><#text#></div>\ + <p class="comment-opts comment">\ + <a href="#" class="reply hidden" id="rl<%id%>">reply ▹</a>\ + <a href="#" class="close-reply" id="cr<%id%>">reply ▿</a>\ + <a href="#" id="sp<%id%>" class="show-proposal">proposal ▹</a>\ + <a href="#" id="hp<%id%>" class="hide-proposal">proposal ▿</a>\ + <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\ + <span id="cm<%id%>" class="moderation hidden">\ + <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\ + </span>\ + </p>\ + <pre class="proposal" id="pr<%id%>">\ +<#proposal_diff#>\ + </pre>\ + <ul class="comment-children" id="cl<%id%>"></ul>\ + </div>\ + <div class="clearleft"></div>\ + </div>\ + </div>'; 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/genome_results.txt Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,216 @@ +BamQC report +----------------------------------- + +>>>>>>> Input + + bam file = ../qualimap2/test-data/test.bam + outfile = /Users/scott/qualimap_results/../qualimap2/test-data/test_stats/genome_results.txt + + +>>>>>>> Reference + + number of bases = 3,101,976,562 bp + number of contigs = 85 + + +>>>>>>> Globals + + number of windows = 484 + + number of reads = 61,169 + number of mapped reads = 60,246 (98.49%) + number of supplementary alignments = 1,169 (1.91%) + number of secondary alignments = 0 + + number of mapped paired reads (first in pair) = 30,268 + number of mapped paired reads (second in pair) = 29,978 + number of mapped paired reads (both in pair) = 59,810 + number of mapped paired reads (singletons) = 436 + + number of mapped bases = 13,270,629 bp + number of sequenced bases = 13,248,971 bp + number of aligned bases = 0 bp + number of duplicated reads (flagged) = 48 + + +>>>>>>> Insert size + + mean insert size = 75,226.7884 + std insert size = 2,849,315.9638 + median insert size = 427 + + +>>>>>>> Mapping quality + + mean mapping quality = 49.9688 + + +>>>>>>> ACTG content + + number of A's = 3,912,917 bp (29.53%) + number of C's = 2,699,395 bp (20.37%) + number of T's = 3,942,019 bp (29.75%) + number of G's = 2,694,640 bp (20.34%) + number of N's = 14,397 bp (0.11%) + + GC percentage = 40.71% + + +>>>>>>> Mismatches and indels + + general error rate = 0.0149 + number of mismatches = 190,508 + number of insertions = 2,279 + mapped reads with insertion percentage = 3.3% + number of deletions = 2,316 + mapped reads with deletion percentage = 3.41% + homopolymer indels = 50.79% + + +>>>>>>> Coverage + + mean coverageData = 0.0043X + std coverageData = 0.0869X + + There is a 0.35% of reference with a coverageData >= 1X + There is a 0.06% of reference with a coverageData >= 2X + There is a 0% of reference with a coverageData >= 3X + There is a 0% of reference with a coverageData >= 4X + There is a 0% of reference with a coverageData >= 5X + There is a 0% of reference with a coverageData >= 6X + There is a 0% of reference with a coverageData >= 7X + There is a 0% of reference with a coverageData >= 8X + There is a 0% of reference with a coverageData >= 9X + There is a 0% of reference with a coverageData >= 10X + There is a 0% of reference with a coverageData >= 11X + There is a 0% of reference with a coverageData >= 12X + There is a 0% of reference with a coverageData >= 13X + There is a 0% of reference with a coverageData >= 14X + There is a 0% of reference with a coverageData >= 15X + There is a 0% of reference with a coverageData >= 16X + There is a 0% of reference with a coverageData >= 17X + There is a 0% of reference with a coverageData >= 18X + There is a 0% of reference with a coverageData >= 19X + There is a 0% of reference with a coverageData >= 20X + There is a 0% of reference with a coverageData >= 21X + There is a 0% of reference with a coverageData >= 22X + There is a 0% of reference with a coverageData >= 23X + There is a 0% of reference with a coverageData >= 24X + There is a 0% of reference with a coverageData >= 25X + There is a 0% of reference with a coverageData >= 26X + There is a 0% of reference with a coverageData >= 27X + There is a 0% of reference with a coverageData >= 28X + There is a 0% of reference with a coverageData >= 29X + There is a 0% of reference with a coverageData >= 30X + There is a 0% of reference with a coverageData >= 31X + There is a 0% of reference with a coverageData >= 32X + There is a 0% of reference with a coverageData >= 33X + There is a 0% of reference with a coverageData >= 34X + There is a 0% of reference with a coverageData >= 35X + There is a 0% of reference with a coverageData >= 36X + There is a 0% of reference with a coverageData >= 37X + There is a 0% of reference with a coverageData >= 38X + There is a 0% of reference with a coverageData >= 39X + There is a 0% of reference with a coverageData >= 40X + There is a 0% of reference with a coverageData >= 41X + There is a 0% of reference with a coverageData >= 42X + There is a 0% of reference with a coverageData >= 43X + There is a 0% of reference with a coverageData >= 44X + There is a 0% of reference with a coverageData >= 45X + There is a 0% of reference with a coverageData >= 46X + There is a 0% of reference with a coverageData >= 47X + There is a 0% of reference with a coverageData >= 48X + There is a 0% of reference with a coverageData >= 49X + There is a 0% of reference with a coverageData >= 50X + There is a 0% of reference with a coverageData >= 51X + + +>>>>>>> Coverage per contig + + 1 249250621 1063202 0.0042655941868245135 0.11474133265687901 + 2 243199373 1091086 0.004486384921724284 0.08203514966215787 + 3 198022430 906302 0.0045767643594718035 0.07649298211953029 + 4 191154276 899976 0.0047081133565644116 0.08801106637704532 + 5 180915260 759318 0.0041970920529313 0.07387256522488687 + 6 171115067 734471 0.004292263754891905 0.07515753948889856 + 7 159138663 654165 0.004110660399352482 0.07727661927489896 + 8 146364022 676934 0.004625002720955564 0.1183980596848048 + 9 141213431 525097 0.003718463578722905 0.07655614932683714 + 10 135534747 724777 0.005347536451298352 0.13105872546587533 + 11 135006516 589118 0.004363626419335197 0.0819970313239365 + 12 133851895 581268 0.004342620625580235 0.07449887187508934 + 13 115169878 424915 0.003689462968780778 0.06887087591436021 + 14 107349540 385363 0.0035897964723463184 0.0679903442535131 + 15 102531392 361006 0.0035209314236170713 0.0670979108943531 + 16 90354753 405846 0.004491695085481557 0.08332772067436123 + 17 81195210 351366 0.004327422762993039 0.07646727778547596 + 18 78077248 355035 0.004547227381784768 0.08165845973392132 + 19 59128983 263166 0.004450710745354778 0.08882137386093936 + 20 63025520 262814 0.00416996162824202 0.08047946626572652 + 21 48129895 179259 0.0037244835044830246 0.07476818927110641 + 22 51304566 150578 0.0029349824341170726 0.0611679626980567 + X 155270560 669025 0.004308769157527351 0.07526511311322369 + Y 59373566 28998 4.883991640320205E-4 0.048961688957033685 + MT 16569 56251 3.3949544329772467 2.090333991172169 + GL000207.1 4262 0 0.0 0.0 + GL000226.1 15008 21953 1.462753198294243 1.7817481720704884 + GL000229.1 19913 0 0.0 0.0 + GL000231.1 27386 1169 0.042686043964069234 0.22782437837143313 + GL000210.1 27682 0 0.0 0.0 + GL000239.1 33824 0 0.0 0.0 + GL000235.1 34474 0 0.0 0.0 + GL000201.1 36148 0 0.0 0.0 + GL000247.1 36422 0 0.0 0.0 + GL000245.1 36651 481 0.01312378925540913 0.11380490064574872 + GL000197.1 37175 0 0.0 0.0 + GL000203.1 37498 459 0.012240652834817857 0.11783916377385595 + GL000246.1 38154 0 0.0 0.0 + GL000249.1 38502 483 0.012544802867383513 0.11129883552132071 + GL000196.1 38914 0 0.0 0.0 + GL000248.1 39786 456 0.011461318051575931 0.1064422671690929 + GL000244.1 39929 0 0.0 0.0 + GL000238.1 39939 410 0.010265655124064198 0.10079817185315403 + GL000202.1 40103 423 0.01054783931376705 0.14172952867532188 + GL000234.1 40531 733 0.01808492265179739 0.16754388053836994 + GL000232.1 40652 543 0.013357276394765326 0.11943134321699386 + GL000206.1 41001 0 0.0 0.0 + GL000240.1 41933 475 0.011327594019030359 0.10560617899658505 + GL000236.1 41934 924 0.022034625840606666 0.14664074791144804 + GL000241.1 42152 930 0.022063010058834695 0.1716172805993474 + GL000243.1 43341 110 0.0025380125054797996 0.050314719496404106 + GL000242.1 43523 444 0.01020150265376927 0.10048597910840303 + GL000230.1 43691 939 0.021491840424801446 0.15435104773307612 + GL000237.1 45867 852 0.018575446399372097 0.1350199955207974 + GL000233.1 45941 0 0.0 0.0 + GL000204.1 81310 1345 0.016541630795720085 0.15485361072846573 + GL000198.1 90085 1750 0.01942609757451296 0.1441201421470368 + GL000208.1 92689 3998 0.04313348941082545 0.26966787890682825 + GL000191.1 106433 0 0.0 0.0 + GL000227.1 128374 476 0.0037079159331328774 0.06077966183326209 + GL000228.1 129120 4339 0.0336043990086741 0.31051049552382226 + GL000214.1 137718 2220 0.016119897181196358 0.13417453858876183 + GL000221.1 155397 2809 0.0180762820389068 0.1740454893979014 + GL000209.1 159169 463 0.002908857880617457 0.057412879155664565 + GL000218.1 161147 1369 0.008495348967092158 0.11158253527221668 + GL000220.1 161802 40235 0.24866812523949025 0.6522381339854945 + GL000213.1 164239 490 0.0029834570351743497 0.05453949045685721 + GL000211.1 166566 384 0.002305392457044055 0.06786361381261032 + GL000199.1 169874 21154 0.1245275910380635 0.5192099824822648 + GL000217.1 172149 2403 0.013958837983374868 0.13067907272830356 + GL000216.1 172294 13420 0.07789011805402393 0.44542525607142536 + GL000215.1 172545 960 0.005563765974093715 0.0995128835326423 + GL000205.1 174588 1778 0.010183975989185969 0.12506909205934466 + GL000219.1 179198 1205 0.006724405406310338 0.0920058264135254 + GL000224.1 179693 2523 0.014040613713388947 0.1395744382666369 + GL000223.1 180455 622 0.0034468427031669946 0.05856157983250805 + GL000195.1 182896 2173 0.011881069022832648 0.12355927053507777 + GL000212.1 186858 1274 0.006818011538173372 0.12426267041345786 + GL000222.1 186861 437 0.0023386367406789004 0.048247704382161936 + GL000200.1 187035 370 0.0019782393669634025 0.0628694305917733 + GL000193.1 189789 3642 0.019189731754738155 0.15465456173194198 + GL000194.1 191469 1260 0.006580699747739843 0.09088955242033304 + GL000225.1 211173 10094 0.04779967135950145 0.2717200747790388 + GL000192.1 547496 3452 0.006305068895480515 0.08493163306317596 + NC_007605 171823 12864 0.07486774180406582 0.29800908736364445 + +
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/qualimapReport.html Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,1046 @@ +<!DOCTYPE HTML> +<html> + <head> + <link rel="stylesheet" href="css/agogo.css" type="text/css" /> + <link rel="stylesheet" href="css/report.css" type="text/css" /> + <title>Qualimap report: BAM QC</title> + + </head> +<body> + <div class="header-wrapper"> + <div class="header"> + <p class="logo"><a href="http://qualimap.bioinfo.cipf.es/"> + <img class="logo" src="css/qualimap_logo_small.png" alt="Logo"/> + </a></p> +<div class="headertitle"><a href="">Qualimap Report: BAM QC</a></div> + </div> +</div> + +<div class="content-wrapper"> +<div class="content"> +<div class="document"> +<div class="documentwrapper"> +<div class="bodywrapper"> +<div class="body"> +<div class=section> +<h2>Input data and parameters<a class="headerlink" name="input" title="Permalink to this headline"> </a></h2> +<div class=summary> + + +<div class=table-summary> +<h3>QualiMap command line</h3> +<table class="summary hovertable"> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>qualimap bamqc -bam ../qualimap2/test-data/test.bam -nw 400 -hm 3</td> +</tr> +</table> +</div> + + +<div class=table-summary> +<h3>Alignment</h3> +<table class="summary hovertable"> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Command line: </td> +<td class=column2>bwa mem -K 100000000 -p -v 3 -t 16 -Y /cromwell_root/broad-references/hg19/v0/Homo_sapiens_assembly19.fasta</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Draw chromosome limits: </td> +<td class=column2>no +</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Analyze overlapping paired-end reads:</td> +<td class=column2>no +</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Program: </td> +<td class=column2>bwamem (0.7.15-r1140)</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Analysis date: </td> +<td class=column2>Thu Jul 26 16:33:35 EDT 2018</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Size of a homopolymer: </td> +<td class=column2>3</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Skip duplicate alignments: </td> +<td class=column2>no +</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Number of windows: </td> +<td class=column2>400</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>BAM file: </td> +<td class=column2>../qualimap2/test-data/test.bam</td> +</tr> +</table> +</div> + +</div> +</div> <!-- summary section --> + +<div class=section> +<h2>Summary<a class="headerlink" name="summary" title="Permalink to this headline"> </a></h2> +<div class=summary> + + +<div class=table-summary> +<h3>Globals</h3> +<table class="summary hovertable"> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Reference size</td> +<td class=column2>3,101,976,562</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Number of reads</td> +<td class=column2>61,169</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Mapped reads</td> +<td class=column2>60,246 / 98.49%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Unmapped reads</td> +<td class=column2>923 / 1.51%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Mapped paired reads</td> +<td class=column2>60,246 / 98.49%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Mapped reads, first in pair</td> +<td class=column2>30,268 / 49.48%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Mapped reads, second in pair</td> +<td class=column2>29,978 / 49.01%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Mapped reads, both in pair</td> +<td class=column2>59,810 / 97.78%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Mapped reads, singletons</td> +<td class=column2>436 / 0.71%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Secondary alignments</td> +<td class=column2>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Supplementary alignments</td> +<td class=column2>1,169 / 1.91%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Read min/max/mean length</td> +<td class=column2>250 / 250 / 250</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Duplicated reads (flagged)</td> +<td class=column2>48 / 0.08%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Clipped reads</td> +<td class=column2>33,606 / 54.94%</td> +</tr> +</table> +</div> + + +<div class=table-summary> +<h3>ACGT Content</h3> +<table class="summary hovertable"> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Number/percentage of A's</td> +<td class=column2>3,912,917 / 29.53%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Number/percentage of C's</td> +<td class=column2>2,699,395 / 20.37%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Number/percentage of T's</td> +<td class=column2>3,942,019 / 29.75%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Number/percentage of G's</td> +<td class=column2>2,694,640 / 20.34%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Number/percentage of N's</td> +<td class=column2>14,397 / 0.11%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>GC Percentage</td> +<td class=column2>40.71%</td> +</tr> +</table> +</div> + + +<div class=table-summary> +<h3>Coverage</h3> +<table class="summary hovertable"> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Mean</td> +<td class=column2>0.0043</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Standard Deviation</td> +<td class=column2>0.0869</td> +</tr> +</table> +</div> + + +<div class=table-summary> +<h3>Mapping Quality</h3> +<table class="summary hovertable"> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Mean Mapping Quality</td> +<td class=column2>49.97</td> +</tr> +</table> +</div> + + +<div class=table-summary> +<h3>Insert size</h3> +<table class="summary hovertable"> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Mean</td> +<td class=column2>75,226.79</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Standard Deviation</td> +<td class=column2>2,849,315.96</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>P25/Median/P75</td> +<td class=column2>339 / 427 / 535</td> +</tr> +</table> +</div> + + +<div class=table-summary> +<h3>Mismatches and indels</h3> +<table class="summary hovertable"> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>General error rate</td> +<td class=column2>1.49%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Mismatches</td> +<td class=column2>190,508</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Insertions</td> +<td class=column2>2,279</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Mapped reads with at least one insertion</td> +<td class=column2>3.3%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Deletions</td> +<td class=column2>2,316</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Mapped reads with at least one deletion</td> +<td class=column2>3.41%</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td class=column1>Homopolymer indels</td> +<td class=column2>50.79%</td> +</tr> +</table> +</div> + + +<div class=table-summary> +<h3>Chromosome stats</h3> +<table class="summary hovertable"> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td><b>Name</b></td> +<td><b>Length</b></td> +<td><b>Mapped bases</b></td> +<td><b>Mean coverage</b></td> +<td><b>Standard deviation</b></td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>1</td> +<td>249250621</td> +<td>1063202</td> +<td>0.0043</td> +<td>0.1147</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>2</td> +<td>243199373</td> +<td>1091086</td> +<td>0.0045</td> +<td>0.082</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>3</td> +<td>198022430</td> +<td>906302</td> +<td>0.0046</td> +<td>0.0765</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>4</td> +<td>191154276</td> +<td>899976</td> +<td>0.0047</td> +<td>0.088</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>5</td> +<td>180915260</td> +<td>759318</td> +<td>0.0042</td> +<td>0.0739</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>6</td> +<td>171115067</td> +<td>734471</td> +<td>0.0043</td> +<td>0.0752</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>7</td> +<td>159138663</td> +<td>654165</td> +<td>0.0041</td> +<td>0.0773</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>8</td> +<td>146364022</td> +<td>676934</td> +<td>0.0046</td> +<td>0.1184</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>9</td> +<td>141213431</td> +<td>525097</td> +<td>0.0037</td> +<td>0.0766</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>10</td> +<td>135534747</td> +<td>724777</td> +<td>0.0053</td> +<td>0.1311</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>11</td> +<td>135006516</td> +<td>589118</td> +<td>0.0044</td> +<td>0.082</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>12</td> +<td>133851895</td> +<td>581268</td> +<td>0.0043</td> +<td>0.0745</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>13</td> +<td>115169878</td> +<td>424915</td> +<td>0.0037</td> +<td>0.0689</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>14</td> +<td>107349540</td> +<td>385363</td> +<td>0.0036</td> +<td>0.068</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>15</td> +<td>102531392</td> +<td>361006</td> +<td>0.0035</td> +<td>0.0671</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>16</td> +<td>90354753</td> +<td>405846</td> +<td>0.0045</td> +<td>0.0833</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>17</td> +<td>81195210</td> +<td>351366</td> +<td>0.0043</td> +<td>0.0765</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>18</td> +<td>78077248</td> +<td>355035</td> +<td>0.0045</td> +<td>0.0817</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>19</td> +<td>59128983</td> +<td>263166</td> +<td>0.0045</td> +<td>0.0888</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>20</td> +<td>63025520</td> +<td>262814</td> +<td>0.0042</td> +<td>0.0805</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>21</td> +<td>48129895</td> +<td>179259</td> +<td>0.0037</td> +<td>0.0748</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>22</td> +<td>51304566</td> +<td>150578</td> +<td>0.0029</td> +<td>0.0612</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>X</td> +<td>155270560</td> +<td>669025</td> +<td>0.0043</td> +<td>0.0753</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>Y</td> +<td>59373566</td> +<td>28998</td> +<td>0.0005</td> +<td>0.049</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>MT</td> +<td>16569</td> +<td>56251</td> +<td>3.395</td> +<td>2.0903</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000207.1</td> +<td>4262</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000226.1</td> +<td>15008</td> +<td>21953</td> +<td>1.4628</td> +<td>1.7817</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000229.1</td> +<td>19913</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000231.1</td> +<td>27386</td> +<td>1169</td> +<td>0.0427</td> +<td>0.2278</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000210.1</td> +<td>27682</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000239.1</td> +<td>33824</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000235.1</td> +<td>34474</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000201.1</td> +<td>36148</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000247.1</td> +<td>36422</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000245.1</td> +<td>36651</td> +<td>481</td> +<td>0.0131</td> +<td>0.1138</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000197.1</td> +<td>37175</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000203.1</td> +<td>37498</td> +<td>459</td> +<td>0.0122</td> +<td>0.1178</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000246.1</td> +<td>38154</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000249.1</td> +<td>38502</td> +<td>483</td> +<td>0.0125</td> +<td>0.1113</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000196.1</td> +<td>38914</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000248.1</td> +<td>39786</td> +<td>456</td> +<td>0.0115</td> +<td>0.1064</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000244.1</td> +<td>39929</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000238.1</td> +<td>39939</td> +<td>410</td> +<td>0.0103</td> +<td>0.1008</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000202.1</td> +<td>40103</td> +<td>423</td> +<td>0.0105</td> +<td>0.1417</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000234.1</td> +<td>40531</td> +<td>733</td> +<td>0.0181</td> +<td>0.1675</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000232.1</td> +<td>40652</td> +<td>543</td> +<td>0.0134</td> +<td>0.1194</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000206.1</td> +<td>41001</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000240.1</td> +<td>41933</td> +<td>475</td> +<td>0.0113</td> +<td>0.1056</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000236.1</td> +<td>41934</td> +<td>924</td> +<td>0.022</td> +<td>0.1466</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000241.1</td> +<td>42152</td> +<td>930</td> +<td>0.0221</td> +<td>0.1716</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000243.1</td> +<td>43341</td> +<td>110</td> +<td>0.0025</td> +<td>0.0503</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000242.1</td> +<td>43523</td> +<td>444</td> +<td>0.0102</td> +<td>0.1005</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000230.1</td> +<td>43691</td> +<td>939</td> +<td>0.0215</td> +<td>0.1544</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000237.1</td> +<td>45867</td> +<td>852</td> +<td>0.0186</td> +<td>0.135</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000233.1</td> +<td>45941</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000204.1</td> +<td>81310</td> +<td>1345</td> +<td>0.0165</td> +<td>0.1549</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000198.1</td> +<td>90085</td> +<td>1750</td> +<td>0.0194</td> +<td>0.1441</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000208.1</td> +<td>92689</td> +<td>3998</td> +<td>0.0431</td> +<td>0.2697</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000191.1</td> +<td>106433</td> +<td>0</td> +<td>0</td> +<td>0</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000227.1</td> +<td>128374</td> +<td>476</td> +<td>0.0037</td> +<td>0.0608</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000228.1</td> +<td>129120</td> +<td>4339</td> +<td>0.0336</td> +<td>0.3105</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000214.1</td> +<td>137718</td> +<td>2220</td> +<td>0.0161</td> +<td>0.1342</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000221.1</td> +<td>155397</td> +<td>2809</td> +<td>0.0181</td> +<td>0.174</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000209.1</td> +<td>159169</td> +<td>463</td> +<td>0.0029</td> +<td>0.0574</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000218.1</td> +<td>161147</td> +<td>1369</td> +<td>0.0085</td> +<td>0.1116</td> 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+<td>0.014</td> +<td>0.1396</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000223.1</td> +<td>180455</td> +<td>622</td> +<td>0.0034</td> +<td>0.0586</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000195.1</td> +<td>182896</td> +<td>2173</td> +<td>0.0119</td> +<td>0.1236</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000212.1</td> +<td>186858</td> +<td>1274</td> +<td>0.0068</td> +<td>0.1243</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000222.1</td> +<td>186861</td> +<td>437</td> +<td>0.0023</td> +<td>0.0482</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000200.1</td> +<td>187035</td> +<td>370</td> +<td>0.002</td> +<td>0.0629</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000193.1</td> +<td>189789</td> +<td>3642</td> +<td>0.0192</td> +<td>0.1547</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000194.1</td> +<td>191469</td> +<td>1260</td> +<td>0.0066</td> +<td>0.0909</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000225.1</td> +<td>211173</td> +<td>10094</td> +<td>0.0478</td> +<td>0.2717</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>GL000192.1</td> +<td>547496</td> +<td>3452</td> +<td>0.0063</td> +<td>0.0849</td> +</tr> +<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';"> +<td>NC_007605</td> +<td>171823</td> +<td>12864</td> +<td>0.0749</td> +<td>0.298</td> +</tr> +</table> +</div> + +</div> +</div> <!-- summary section --> + + + +<div class=section> + +<h2>Coverage across reference<a class="headerlink" name="genome_coverage_across_reference.png" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_coverage_across_reference.png"></div> + +</div><!-- graph section --> + + +<div class=section> + +<h2>Coverage Histogram<a class="headerlink" name="genome_coverage_histogram.png" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_coverage_histogram.png"></div> + +</div><!-- graph section --> + + +<div class=section> + +<h2>Coverage Histogram (0-50X)<a class="headerlink" name="genome_coverage_0to50_histogram.png" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_coverage_0to50_histogram.png"></div> + +</div><!-- graph section --> + + +<div class=section> + +<h2>Genome Fraction Coverage<a class="headerlink" name="genome_coverage_quotes.png" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_coverage_quotes.png"></div> + +</div><!-- graph section --> + + +<div class=section> + +<h2>Duplication Rate Histogram<a class="headerlink" name="genome_uniq_read_starts_histogram.png" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_uniq_read_starts_histogram.png"></div> + +</div><!-- graph section --> + + +<div class=section> + +<h2>Mapped Reads Nucleotide Content<a class="headerlink" name="genome_reads_content_per_read_position.png" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_reads_content_per_read_position.png"></div> + +</div><!-- graph section --> + + +<div class=section> + +<h2>Mapped Reads GC-content Distribution<a class="headerlink" name="genome_gc_content_per_window.png" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_gc_content_per_window.png"></div> + +</div><!-- graph section --> + + +<div class=section> + +<h2>Mapped Reads Clipping Profile<a class="headerlink" name="genome_reads_clipping_profile.png" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_reads_clipping_profile.png"></div> + +</div><!-- graph section --> + + +<div class=section> + +<h2>Homopolymer Indels<a class="headerlink" name="genome_homopolymer_indels" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_homopolymer_indels.png"></div> + +</div><!-- graph section --> + + +<div class=section> + +<h2>Mapping Quality Across Reference<a class="headerlink" name="genome_mapping_quality_across_reference.png" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_mapping_quality_across_reference.png"></div> + +</div><!-- graph section --> + + +<div class=section> + +<h2>Mapping Quality Histogram<a class="headerlink" name="genome_mapping_quality_histogram.png" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_mapping_quality_histogram.png"></div> + +</div><!-- graph section --> + + +<div class=section> + +<h2>Insert Size Across Reference<a class="headerlink" name="genome_insert_size_across_reference.png" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_insert_size_across_reference.png"></div> + +</div><!-- graph section --> + + +<div class=section> + +<h2>Insert Size Histogram<a class="headerlink" name="genome_insert_size_histogram.png" title="Permalink to this headline"> </a></h2> + +<div><img width=100% src="images_qualimapReport/genome_insert_size_histogram.png"></div> + +</div><!-- graph section --> + + +</div> + +</div> + +</div> + +</div> + + +<div class="sidebar"> +<h3>Contents</h3> +<li class="toctree-l1"><a class="reference internal" href="#input">Input data & parameters</a></li> +<li class="toctree-l1"><a class="reference internal" href="#summary">Summary</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_across_reference.png">Coverage across reference</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_histogram.png">Coverage Histogram</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_0to50_histogram.png">Coverage Histogram (0-50X)</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_quotes.png">Genome Fraction Coverage</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_uniq_read_starts_histogram.png">Duplication Rate Histogram</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_reads_content_per_read_position.png">Mapped Reads Nucleotide Content</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_gc_content_per_window.png">Mapped Reads GC-content Distribution</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_reads_clipping_profile.png">Mapped Reads Clipping Profile</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_homopolymer_indels">Homopolymer Indels</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_across_reference.png">Mapping Quality Across Reference</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_histogram.png">Mapping Quality Histogram</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_across_reference.png">Insert Size Across Reference</a></li> +<li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_histogram.png">Insert Size Histogram</a></li> +</div> <!-- sidebar --> + +<div class="clearer"></div> +</div> + +</div> + + +<div class="footer-wrapper"> +<div class="footer"> +<div class="left"> +<div class="footer"> +2018/07/26 16:33:36 +</div> +</div> +<div class="right"> +<div class="footer"> +Generated by QualiMap v.2.2.2-dev +</div +</div> +<div class="clearer"></div> +</div> <!-- footer --> +</div> +</body>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/raw_data_qualimapReport/coverage_across_reference.txt Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,485 @@ +#Position (bp) Coverage +3877471.5 0.005025569501357973 +1.16324135E7 0.003507053953466061 +1.93873555E7 0.004769861592775291 +2.71422975E7 0.0038027363712069026 +3.48972395E7 0.004562252045211944 +4.26521815E7 0.004270953928475545 +5.04071235E7 0.004586623600795467 +5.81620655E7 0.004900616922731337 +6.59170075E7 0.005221831446321584 +7.36719495E7 0.004432915165580864 +8.14268915E7 0.005243237151225631 +8.91818335E7 0.004602871304517816 +9.69367755E7 0.004384429954472902 +1.046917175E8 0.00441640956179943 +1.124466595E8 0.004874569016763762 +1.202016015E8 0.007699606263979795 +1.279565435E8 0.0 +1.357114855E8 0.0 +1.434664275E8 0.00445844727143027 +1.512213695E8 0.004682433472745508 +1.589763115E8 0.004239748021326271 +1.667312535E8 0.0042713407785641725 +1.744861955E8 0.004625824409776372 +1.822411375E8 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/raw_data_qualimapReport/coverage_histogram.txt Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,101 @@ +#Coverage Number of genomic locations +0.0 3.090980583E9 +1.0 9071159.0 +2.0 1841034.0 +3.0 36125.0 +4.0 16010.0 +5.0 8664.0 +6.0 6016.0 +7.0 3740.0 +8.0 2032.0 +9.0 1944.0 +10.0 1180.0 +11.0 969.0 +12.0 658.0 +13.0 739.0 +14.0 694.0 +15.0 622.0 +16.0 523.0 +17.0 397.0 +18.0 369.0 +19.0 256.0 +20.0 171.0 +21.0 173.0 +22.0 246.0 +23.0 250.0 +24.0 178.0 +25.0 133.0 +26.0 92.0 +27.0 111.0 +28.0 70.0 +29.0 82.0 +30.0 94.0 +31.0 119.0 +32.0 130.0 +33.0 97.0 +34.0 121.0 +35.0 101.0 +36.0 75.0 +37.0 29.0 +38.0 51.0 +39.0 27.0 +40.0 38.0 +41.0 32.0 +42.0 6.0 +43.0 1.0 +44.0 2.0 +45.0 4.0 +46.0 1.0 +47.0 2.0 +48.0 16.0 +49.0 9.0 +50.0 3.0 +51.0 11.0 +53.0 4.0 +54.0 4.0 +55.0 4.0 +56.0 1.0 +57.0 5.0 +58.0 5.0 +59.0 2.0 +60.0 4.0 +61.0 3.0 +62.0 12.0 +63.0 1.0 +64.0 5.0 +65.0 1.0 +66.0 6.0 +67.0 11.0 +68.0 8.0 +69.0 10.0 +70.0 7.0 +71.0 27.0 +72.0 23.0 +73.0 14.0 +74.0 18.0 +75.0 6.0 +76.0 12.0 +77.0 9.0 +78.0 12.0 +79.0 6.0 +80.0 11.0 +81.0 10.0 +82.0 2.0 +83.0 7.0 +84.0 6.0 +85.0 4.0 +86.0 2.0 +87.0 4.0 +88.0 4.0 +89.0 12.0 +90.0 6.0 +91.0 18.0 +92.0 5.0 +93.0 14.0 +94.0 11.0 +95.0 3.0 +96.0 3.0 +97.0 7.0 +98.0 13.0 +99.0 7.0 +100.0 4.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/raw_data_qualimapReport/duplication_rate_histogram.txt Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,51 @@ +#Duplication rate Coverage +1.0 55470.0 +2.0 2253.0 +3.0 35.0 +4.0 17.0 +5.0 4.0 +6.0 4.0 +7.0 1.0 +8.0 1.0 +9.0 0.0 +10.0 0.0 +11.0 0.0 +12.0 0.0 +13.0 0.0 +14.0 0.0 +15.0 0.0 +16.0 0.0 +17.0 0.0 +18.0 1.0 +19.0 0.0 +20.0 1.0 +21.0 0.0 +22.0 0.0 +23.0 0.0 +24.0 0.0 +25.0 0.0 +26.0 0.0 +27.0 0.0 +28.0 0.0 +29.0 0.0 +30.0 0.0 +31.0 0.0 +32.0 0.0 +33.0 0.0 +34.0 0.0 +35.0 0.0 +36.0 0.0 +37.0 0.0 +38.0 0.0 +39.0 0.0 +40.0 0.0 +41.0 0.0 +42.0 0.0 +43.0 0.0 +44.0 0.0 +45.0 0.0 +46.0 0.0 +47.0 0.0 +48.0 0.0 +49.0 0.0 +50.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/raw_data_qualimapReport/genome_fraction_coverage.txt Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,52 @@ +#Coverage (X) Coverage +1.0 0.35448298142235046 +2.0 0.062051403726883336 +3.0 0.0027010520010435357 +4.0 0.0015364719573796037 +5.0 0.0010203494245359934 +6.0 7.410436391239728E-4 +7.0 5.471027798051864E-4 +8.0 4.265344929308412E-4 +9.0 3.610278728984895E-4 +10.0 2.9835815372791785E-4 +11.0 2.603178920992377E-4 +12.0 2.2907974503993955E-4 +13.0 2.078674635583866E-4 +14.0 1.8404394377569133E-4 +15.0 1.616711119396541E-4 +16.0 1.416193808125854E-4 +17.0 1.247591631567957E-4 +18.0 1.1196087174880631E-4 +19.0 1.0006523061178996E-4 +20.0 9.181242808153911E-5 +21.0 8.62998139012916E-5 +22.0 8.072272468950814E-5 +23.0 7.279229726009362E-5 +24.0 6.473291979602891E-5 +25.0 5.8994643040932715E-5 +26.0 5.4707054232494556E-5 +27.0 5.174120332185339E-5 +28.0 4.8162839732412976E-5 +29.0 4.5906214040769555E-5 +30.0 4.3262738230964715E-5 +31.0 4.0232412302998455E-5 +32.0 3.639614863004681E-5 +33.0 3.220527234759629E-5 +34.0 2.907823389364239E-5 +35.0 2.5177495203365652E-5 +36.0 2.1921506700550708E-5 +37.0 1.950369346559455E-5 +38.0 1.8568805685958978E-5 +39.0 1.692469268732566E-5 +40.0 1.605427992501518E-5 +41.0 1.4829254553205828E-5 +42.0 1.3797654233371759E-5 +43.0 1.3604229167185622E-5 +44.0 1.3571991658523075E-5 +45.0 1.350751664119798E-5 +46.0 1.3378566606547793E-5 +47.0 1.3346329097885246E-5 +48.0 1.3281854080560151E-5 +49.0 1.2766053927748544E-5 +50.0 1.2475916335574766E-5 +51.0 1.2379203809587125E-5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/raw_data_qualimapReport/homopolymer_indels.txt Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,7 @@ +#Type of indel Number of indels +polyA 802 +polyC 318 +polyG 303 +polyT 911 +polyN 0 +Non-poly 2261
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/raw_data_qualimapReport/insert_size_across_reference.txt Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,485 @@ +#Position (bp) insert size +3877471.5 411.0869565217391 +1.16324135E7 444.9 +1.93873555E7 389.5853658536585 +2.71422975E7 449.0735294117647 +3.48972395E7 405.5128205128205 +4.26521815E7 428.4788732394366 +5.04071235E7 462.37179487179486 +5.81620655E7 430.0843373493976 +6.59170075E7 431.6931818181818 +7.36719495E7 482.7323943661972 +8.14268915E7 445.24719101123594 +8.91818335E7 434.9746835443038 +9.69367755E7 422.7142857142857 +1.046917175E8 478.3835616438356 +1.124466595E8 429.1566265060241 +1.202016015E8 359.8496240601504 +1.279565435E8 0.0 +1.357114855E8 0.0 +1.434664275E8 445.6666666666667 +1.512213695E8 430.3164556962025 +1.589763115E8 424.7432432432432 +1.667312535E8 470.1449275362319 +1.744861955E8 461.0769230769231 +1.822411375E8 426.3709677419355 +1.899960795E8 455.1463414634146 +1.977510215E8 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460.2266666666667 +6.630475415E8 450.0 +6.708024835E8 455.0149253731343 +6.785574255E8 437.6835443037975 +6.863123675E8 429.4943820224719 +6.903311315E8 453.0 +6.942086025E8 447.6666666666667 +7.018222515E8 469.50666666666666 +7.095771935E8 431.43589743589746 +7.173321355E8 462.2564102564103 +7.250870775E8 423.9 +7.328420195E8 428.7931034482759 +7.405969615E8 332.5042735042735 +7.483519035E8 453.2432432432432 +7.561068455E8 442.97872340425533 +7.638617875E8 434.3098591549296 +7.716167295E8 458.44776119402985 +7.793716715E8 473.7241379310345 +7.871266135E8 455.4788732394366 +7.948815555E8 462.9230769230769 +8.026364975E8 410.36486486486484 +8.103914395E8 461.1142857142857 +8.181463815E8 431.68918918918916 +8.259013235E8 430.62857142857143 +8.336562655E8 449.032967032967 +8.414112075E8 413.9230769230769 +8.491661495E8 438.6707317073171 +8.569210915E8 451.126582278481 +8.646760335E8 446.7887323943662 +8.724309755E8 447.26666666666665 +8.789675735E8 465.11290322580646 +8.828450445E8 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/raw_data_qualimapReport/mapped_reads_clipping_profile.txt Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,251 @@ +#Read position (bp) Clipping profile +0.0 0.9960120426149072 +1.0 0.994615894531623 +2.0 0.9869650030352259 +3.0 0.980263492235462 +4.0 0.9729476762790531 +5.0 0.9589303495228803 +6.0 0.9512236121031519 +7.0 0.9425116480634589 +8.0 0.9344139891804107 +9.0 0.926037100680706 +10.0 0.9134717679311486 +11.0 0.9028051965748579 +12.0 0.8937023110718453 +13.0 0.8816395916322703 +14.0 0.8714756335859617 +15.0 0.8576816905231143 +16.0 0.8478528080167939 +17.0 0.8387499225137814 +18.0 0.8289768859307924 +19.0 0.8200415381977738 +20.0 0.8111620363880868 +21.0 0.7583876388399462 +22.0 0.7320283630275416 +23.0 0.7117562928582558 +24.0 0.6933271381589051 +25.0 0.6742278323795781 +26.0 0.6520570008170259 +27.0 0.6341304594276574 +28.0 0.6150869995716618 +29.0 0.6002319839655185 +30.0 0.5848185091260616 +31.0 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0.613299930025058 +222.0 0.6329018491143674 +223.0 0.6512751578903867 +224.0 0.6719939954463234 +225.0 0.6901997664523487 +226.0 0.7101367610816461 +227.0 0.731023136407577 +228.0 0.7589460980732597 +229.0 0.8156855561779274 +230.0 0.8257936683009046 +231.0 0.8351757834205741 +232.0 0.8447254363102376 +233.0 0.8536607840432561 +234.0 0.864494893169541 +235.0 0.8764459207624533 +236.0 0.8873358758120696 +237.0 0.9009064351815914 +238.0 0.9117963902312077 +239.0 0.921904502354185 +240.0 0.9328503033271325 +241.0 0.9421765725234706 +242.0 0.9499391558665304 +243.0 0.958260198442904 +244.0 0.9655201684759815 +245.0 0.9789790359988406 +246.0 0.9885286888885042 +247.0 0.9952860456115995 +248.0 1.001820018641369 +249.0 1.0029927830313279
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,101 @@ +#GC Content (%) Sample +1.0 0.0 +2.0 0.0 +3.0 0.0 +4.0 0.0 +5.0 0.0 +6.0 0.0 +7.0 0.0 +8.0 0.0 +9.0 0.0 +10.0 0.0 +11.0 0.0 +12.0 0.0 +13.0 0.0 +14.0 7.418947993174568E-5 +15.0 0.0 +16.0 0.0 +17.0 0.0 +18.0 7.418947993174568E-5 +19.0 0.0 +20.0 2.2256843979523704E-4 +21.0 4.451368795904741E-4 +22.0 8.902737591809482E-4 +23.0 5.935158394539654E-4 +24.0 7.418947993174568E-5 +25.0 3.7094739965872836E-4 +26.0 8.90273759180948E-4 +27.0 0.0019289264782253875 +28.0 0.0026708212775428445 +29.0 0.005935158394539654 +30.0 0.008828548111877735 +31.0 0.01595073818532532 +32.0 0.02336968617849989 +33.0 0.031530528970991914 +34.0 0.040062319163142665 +35.0 0.04963276207433786 +36.0 0.055790488908672754 +37.0 0.06536093181986793 +38.0 0.06521255286000445 +39.0 0.07255731137324727 +40.0 0.06639958453891238 +41.0 0.06231916314266636 +42.0 0.06061280510423622 +43.0 0.05133912011276801 +44.0 0.050448846353587054 +45.0 0.04258476148082202 +46.0 0.03561095036723792 +47.0 0.031233771051264927 +48.0 0.026634023295496703 +49.0 0.023295496698568147 +50.0 0.020402106981230062 +51.0 0.016395875064915796 +52.0 0.014318569626826917 +53.0 0.01149936938942058 +54.0 0.01068328511017138 +55.0 0.006825432153720603 +56.0 0.005341642555085689 +57.0 0.0036352845166555386 +58.0 0.004599747755768232 +59.0 0.0032643371169968098 +60.0 0.00222568439795237 +61.0 0.0014837895986349137 +62.0 9.644632391126938E-4 +63.0 8.160842792492024E-4 +64.0 8.902737591809482E-4 +65.0 8.160842792492024E-4 +66.0 2.967579197269827E-4 +67.0 2.967579197269827E-4 +68.0 8.160842792492026E-4 +69.0 2.967579197269827E-4 +70.0 0.0 +71.0 2.967579197269827E-4 +72.0 0.0 +73.0 0.0 +74.0 7.418947993174568E-5 +75.0 0.0 +76.0 7.418947993174568E-5 +77.0 7.418947993174568E-5 +78.0 0.0 +79.0 7.418947993174568E-5 +80.0 7.418947993174568E-5 +81.0 0.0 +82.0 7.418947993174568E-5 +83.0 0.0 +84.0 1.4837895986349135E-4 +85.0 0.0 +86.0 0.0 +87.0 0.0 +88.0 0.0 +89.0 0.0 +90.0 0.0 +91.0 0.0 +92.0 0.0 +93.0 0.0 +94.0 7.418947993174568E-5 +95.0 0.0 +96.0 1.4837895986349135E-4 +97.0 0.0 +98.0 0.0 +99.0 0.0 +100.0 7.418947993174568E-5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,251 @@ +# Position (bp) A C G T N +0.0 26.98356558440027 22.246586970361463 19.975949635707718 30.78446629412181 0.009431515408738298 +1.0 30.18663399000848 22.29239325101329 20.34828918842492 27.1656141012348 0.007069469318503158 +2.0 30.371362130928052 20.32273976463956 18.911046907664485 30.394851196767902 0.0 +3.0 29.318623661958636 19.81121026866231 20.68488979457991 30.182933970440118 0.0023423043590284124 +4.0 30.66738277601345 18.669437698486828 20.598262656454324 28.988417709695497 1.0764991593498972 +5.0 30.957632037144517 19.243180499129426 21.186302959953572 28.61288450377249 0.0 +6.0 30.77314696966191 19.11693240460047 19.915303265221116 30.185360886770184 0.009256473746326337 +7.0 29.493416956812467 19.507021144135212 19.756046945975235 31.243514953077085 0.0 +8.0 29.21588454290573 19.8993427402675 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/raw_data_qualimapReport/mapping_quality_across_reference.txt Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,485 @@ +#Position (bp) mapping quality +3877471.5 55.488825597208326 +1.16324135E7 55.46920616244439 +1.93873555E7 57.128034603947015 +2.71422975E7 59.423906408952185 +3.48972395E7 59.638694177501414 +4.26521815E7 58.783158721053105 +5.04071235E7 59.73550001405719 +5.81620655E7 59.82317650773603 +6.59170075E7 59.575058649215954 +7.36719495E7 58.976350466881925 +8.14268915E7 59.03384078109245 +8.91818335E7 59.2774338142597 +9.69367755E7 59.69559718831799 +1.046917175E8 58.889923793395425 +1.124466595E8 59.626950954975925 +1.202016015E8 50.9672416680623 +1.279565435E8 0.0 +1.357114855E8 0.0 +1.434664275E8 40.42767895878525 +1.512213695E8 53.03100903282662 +1.589763115E8 57.04787250220505 +1.667312535E8 59.71978021978022 +1.744861955E8 58.86438268335517 +1.822411375E8 59.71436631638338 +1.899960795E8 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