# HG changeset patch # User scottx611x # Date 1532637619 14400 # Node ID 418ee04dd1b252fb37f04314642b93dd1544d9ca # Parent 71af3fbe85bead24c99554a8c34556539c33d425 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty diff -r 71af3fbe85be -r 418ee04dd1b2 qualimap_bamqc.py --- 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' ) diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/agogo.css --- /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; +} diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/ajax-loader.gif Binary file test-data/test_stats/css/ajax-loader.gif has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/basic.css --- /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 diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/bgfooter.png Binary file test-data/test_stats/css/bgfooter.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/bgtop.png Binary file test-data/test_stats/css/bgtop.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/comment-bright.png Binary file test-data/test_stats/css/comment-bright.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/comment-close.png Binary file test-data/test_stats/css/comment-close.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/comment.png Binary file test-data/test_stats/css/comment.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/doctools.js --- /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() { + $('\u00B6'). + attr('href', '#' + this.id). + attr('title', _('Permalink to this headline')). + appendTo(this); + }); + $('dt[id]').each(function() { + $('\u00B6'). + 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); + $('

' + _('Hide Search Matches') + '

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diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/minus.png Binary file test-data/test_stats/css/minus.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/plus.png Binary file test-data/test_stats/css/plus.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/pygments.css --- /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; 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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 diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/qualimap_logo_small.png Binary file test-data/test_stats/css/qualimap_logo_small.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/report.css --- /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; +} + + + + diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/searchtools.js --- /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 = $('
').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 = $('

' + _('Searching') + '

').appendTo(this.out); + this.dots = $('').appendTo(this.title); + this.status = $('

').appendTo(this.out); + this.output = $('
    ').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 = $('
  • '); + if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') { + // dirhtml builder + var dirname = item[0] + '/'; + if (dirname.match(/\/index\/$/)) { + dirname = dirname.substring(0, dirname.length-6); + } else if (dirname == 'index/') { + dirname = ''; + } + listItem.append($('').attr('href', + DOCUMENTATION_OPTIONS.URL_ROOT + dirname + + highlightstring + item[2]).html(item[1])); + } else { + // normal html builders + listItem.append($('').attr('href', + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX + + highlightstring + item[2]).html(item[1])); + } + if (item[3]) { + listItem.append($(' (' + item[3] + ')')); + 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 diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/underscore.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/css/underscore.js Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,23 @@ +// Underscore.js 0.5.5 +// (c) 2009 Jeremy Ashkenas, DocumentCloud Inc. +// Underscore is freely distributable under the terms of the MIT license. +// Portions of Underscore are inspired by or borrowed from Prototype.js, +// Oliver Steele's Functional, and John Resig's Micro-Templating. +// For all details and documentation: +// http://documentcloud.github.com/underscore/ +(function(){var j=this,n=j._,i=function(a){this._wrapped=a},m=typeof StopIteration!=="undefined"?StopIteration:"__break__",b=j._=function(a){return new i(a)};if(typeof exports!=="undefined")exports._=b;var k=Array.prototype.slice,o=Array.prototype.unshift,p=Object.prototype.toString,q=Object.prototype.hasOwnProperty,r=Object.prototype.propertyIsEnumerable;b.VERSION="0.5.5";b.each=function(a,c,d){try{if(a.forEach)a.forEach(c,d);else if(b.isArray(a)||b.isArguments(a))for(var e=0,f=a.length;e=e.computed&&(e={value:f,computed:g})});return e.value};b.min=function(a,c,d){if(!c&&b.isArray(a))return Math.min.apply(Math,a);var e={computed:Infinity};b.each(a,function(f,g,h){g=c?c.call(d,f,g,h):f;gf?1:0}),"value")};b.sortedIndex=function(a,c,d){d=d||b.identity;for(var e=0,f=a.length;e>1;d(a[g])=0})})};b.zip=function(){for(var a=b.toArray(arguments),c=b.max(b.pluck(a,"length")),d=new Array(c),e=0;e0?f-c:c-f)>=0)return e;e[g++]=f}};b.bind=function(a,c){var d=b.rest(arguments,2);return function(){return a.apply(c||j,d.concat(b.toArray(arguments)))}};b.bindAll=function(a){var c=b.rest(arguments);if(c.length==0)c=b.functions(a);b.each(c,function(d){a[d]=b.bind(a[d],a)}); +return a};b.delay=function(a,c){var d=b.rest(arguments,2);return setTimeout(function(){return a.apply(a,d)},c)};b.defer=function(a){return b.delay.apply(b,[a,1].concat(b.rest(arguments)))};b.wrap=function(a,c){return function(){var d=[a].concat(b.toArray(arguments));return c.apply(c,d)}};b.compose=function(){var a=b.toArray(arguments);return function(){for(var c=b.toArray(arguments),d=a.length-1;d>=0;d--)c=[a[d].apply(this,c)];return c[0]}};b.keys=function(a){if(b.isArray(a))return b.range(0,a.length); +var c=[];for(var d in a)q.call(a,d)&&c.push(d);return c};b.values=function(a){return b.map(a,b.identity)};b.functions=function(a){return b.select(b.keys(a),function(c){return b.isFunction(a[c])}).sort()};b.extend=function(a,c){for(var d in c)a[d]=c[d];return a};b.clone=function(a){if(b.isArray(a))return a.slice(0);return b.extend({},a)};b.tap=function(a,c){c(a);return a};b.isEqual=function(a,c){if(a===c)return true;var d=typeof a;if(d!=typeof c)return false;if(a==c)return true;if(!a&&c||a&&!c)return false; +if(a.isEqual)return a.isEqual(c);if(b.isDate(a)&&b.isDate(c))return a.getTime()===c.getTime();if(b.isNaN(a)&&b.isNaN(c))return true;if(b.isRegExp(a)&&b.isRegExp(c))return a.source===c.source&&a.global===c.global&&a.ignoreCase===c.ignoreCase&&a.multiline===c.multiline;if(d!=="object")return false;if(a.length&&a.length!==c.length)return false;d=b.keys(a);var e=b.keys(c);if(d.length!=e.length)return false;for(var f in a)if(!b.isEqual(a[f],c[f]))return false;return true};b.isEmpty=function(a){return b.keys(a).length== +0};b.isElement=function(a){return!!(a&&a.nodeType==1)};b.isArray=function(a){return!!(a&&a.concat&&a.unshift)};b.isArguments=function(a){return a&&b.isNumber(a.length)&&!b.isArray(a)&&!r.call(a,"length")};b.isFunction=function(a){return!!(a&&a.constructor&&a.call&&a.apply)};b.isString=function(a){return!!(a===""||a&&a.charCodeAt&&a.substr)};b.isNumber=function(a){return p.call(a)==="[object Number]"};b.isDate=function(a){return!!(a&&a.getTimezoneOffset&&a.setUTCFullYear)};b.isRegExp=function(a){return!!(a&& +a.test&&a.exec&&(a.ignoreCase||a.ignoreCase===false))};b.isNaN=function(a){return b.isNumber(a)&&isNaN(a)};b.isNull=function(a){return a===null};b.isUndefined=function(a){return typeof a=="undefined"};b.noConflict=function(){j._=n;return this};b.identity=function(a){return a};b.breakLoop=function(){throw m;};var s=0;b.uniqueId=function(a){var c=s++;return a?a+c:c};b.template=function(a,c){a=new Function("obj","var p=[],print=function(){p.push.apply(p,arguments);};with(obj){p.push('"+a.replace(/[\r\t\n]/g, +" ").replace(/'(?=[^%]*%>)/g,"\t").split("'").join("\\'").split("\t").join("'").replace(/<%=(.+?)%>/g,"',$1,'").split("<%").join("');").split("%>").join("p.push('")+"');}return p.join('');");return c?a(c):a};b.forEach=b.each;b.foldl=b.inject=b.reduce;b.foldr=b.reduceRight;b.filter=b.select;b.every=b.all;b.some=b.any;b.head=b.first;b.tail=b.rest;b.methods=b.functions;var l=function(a,c){return c?b(a).chain():a};b.each(b.functions(b),function(a){var c=b[a];i.prototype[a]=function(){var d=b.toArray(arguments); +o.call(d,this._wrapped);return l(c.apply(b,d),this._chain)}});b.each(["pop","push","reverse","shift","sort","splice","unshift"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){c.apply(this._wrapped,arguments);return l(this._wrapped,this._chain)}});b.each(["concat","join","slice"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){return l(c.apply(this._wrapped,arguments),this._chain)}});i.prototype.chain=function(){this._chain=true;return this};i.prototype.value=function(){return this._wrapped}})(); diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/up-pressed.png Binary file test-data/test_stats/css/up-pressed.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/up.png Binary file test-data/test_stats/css/up.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/css/websupport.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_stats/css/websupport.js Thu Jul 26 16:40:19 2018 -0400 @@ -0,0 +1,808 @@ +/* + * websupport.js + * ~~~~~~~~~~~~~ + * + * sphinx.websupport utilties for all documentation. + * + * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +(function($) { + $.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('
  • No comments yet.
    • '); + 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; iThank you! Your comment will show up ' + + 'once it is has been approved by a moderator.'); + } + // 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 = '\ +
    \ +

    \ + Sort by:\ + best rated\ + newest\ + oldest\ +

    \ +
    Comments
    \ +
    \ + loading comments...
    \ +
      \ +
      \ +

      Add a comment\ + (markup):

      \ +
      \ + reStructured text markup: *emph*, **strong**, \ + ``code``, \ + code blocks: :: and an indented block after blank line
      \ +
      \ + \ +

      \ + \ + Propose a change ▹\ + \ + \ + Propose a change ▿\ + \ +

      \ + \ + \ + \ + \ +
      \ +
      \ +
      '; + + var commentTemplate = '\ +
      \ +
      \ +
      \ + \ + \ + \ + \ + \ + \ +
      \ +
      \ + \ + \ + \ + \ + \ + \ +
      \ +
      \ +
      \ +

      \ + <%username%>\ + <%pretty_rating%>\ + <%time.delta%>\ +

      \ +
      <#text#>
      \ +

      \ + \ + reply ▿\ + proposal ▹\ + proposal ▿\ + \ + \ +

      \ + 
      \
+<#proposal_diff#>\
+
      \ +
        \ +
        \ +
        \ +
        \ + '; + + var replyTemplate = '\ +
      • \ +
        \ +
        \ + \ + \ + \ + \ + \ +
        \ +
        \ +
        • '; + + $(document).ready(function() { + init(); + }); +})(jQuery); + +$(document).ready(function() { + // add comment anchors for all paragraphs that are commentable + $('.sphinx-has-comment').comment(); + + // highlight search words in search results + $("div.context").each(function() { + var params = $.getQueryParameters(); + var terms = (params.q) ? params.q[0].split(/\s+/) : []; + var result = $(this); + $.each(terms, function() { + result.highlightText(this.toLowerCase(), 'highlighted'); + }); + }); + + // directly open comment window if requested + var anchor = document.location.hash; + if (anchor.substring(0, 9) == '#comment-') { + $('#ao' + anchor.substring(9)).click(); + document.location.hash = '#s' + anchor.substring(9); + } +}); diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/genome_results.txt --- /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 + + diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_coverage_0to50_histogram.png Binary file test-data/test_stats/images_qualimapReport/genome_coverage_0to50_histogram.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_coverage_across_reference.png Binary file test-data/test_stats/images_qualimapReport/genome_coverage_across_reference.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_coverage_histogram.png Binary file test-data/test_stats/images_qualimapReport/genome_coverage_histogram.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_coverage_quotes.png Binary file test-data/test_stats/images_qualimapReport/genome_coverage_quotes.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_gc_content_per_window.png Binary file test-data/test_stats/images_qualimapReport/genome_gc_content_per_window.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_homopolymer_indels.png Binary file test-data/test_stats/images_qualimapReport/genome_homopolymer_indels.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_insert_size_across_reference.png Binary file test-data/test_stats/images_qualimapReport/genome_insert_size_across_reference.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_insert_size_histogram.png Binary file test-data/test_stats/images_qualimapReport/genome_insert_size_histogram.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_mapping_quality_across_reference.png Binary file test-data/test_stats/images_qualimapReport/genome_mapping_quality_across_reference.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_mapping_quality_histogram.png Binary file test-data/test_stats/images_qualimapReport/genome_mapping_quality_histogram.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_reads_clipping_profile.png Binary file test-data/test_stats/images_qualimapReport/genome_reads_clipping_profile.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_reads_content_per_read_position.png Binary file test-data/test_stats/images_qualimapReport/genome_reads_content_per_read_position.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/images_qualimapReport/genome_uniq_read_starts_histogram.png Binary file test-data/test_stats/images_qualimapReport/genome_uniq_read_starts_histogram.png has changed diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/qualimapReport.html --- /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 @@ + + + + + + Qualimap report: BAM QC + + + +
        +
        + +
        Qualimap Report: BAM QC
        +
        +
        + +
        +
        +
        +
        +
        +
        +
        +

        Input data and parameters 

        +
        + + +
        +

        QualiMap command line

        + + + + +
        qualimap bamqc -bam ../qualimap2/test-data/test.bam -nw 400 -hm 3
        +
        + + +
        +

        Alignment

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Command line: bwa mem -K 100000000 -p -v 3 -t 16 -Y /cromwell_root/broad-references/hg19/v0/Homo_sapiens_assembly19.fasta
        Draw chromosome limits: no +
        Analyze overlapping paired-end reads:no +
        Program: bwamem (0.7.15-r1140)
        Analysis date: Thu Jul 26 16:33:35 EDT 2018
        Size of a homopolymer: 3
        Skip duplicate alignments: no +
        Number of windows: 400
        BAM file: ../qualimap2/test-data/test.bam
        +
        + +
        +
        + +
        +

        Summary 

        +
        + + +
        +

        Globals

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Reference size3,101,976,562
        Number of reads61,169
        Mapped reads60,246 / 98.49%
        Unmapped reads923 / 1.51%
        Mapped paired reads60,246 / 98.49%
        Mapped reads, first in pair30,268 / 49.48%
        Mapped reads, second in pair29,978 / 49.01%
        Mapped reads, both in pair59,810 / 97.78%
        Mapped reads, singletons436 / 0.71%
        Secondary alignments0
        Supplementary alignments1,169 / 1.91%
        Read min/max/mean length250 / 250 / 250
        Duplicated reads (flagged)48 / 0.08%
        Clipped reads33,606 / 54.94%
        +
        + + +
        +

        ACGT Content

        + + + + + + + + + + + + + + + + + + + + + + + + + +
        Number/percentage of A's3,912,917 / 29.53%
        Number/percentage of C's2,699,395 / 20.37%
        Number/percentage of T's3,942,019 / 29.75%
        Number/percentage of G's2,694,640 / 20.34%
        Number/percentage of N's14,397 / 0.11%
        GC Percentage40.71%
        +
        + + +
        +

        Coverage

        + + + + + + + + + +
        Mean0.0043
        Standard Deviation0.0869
        +
        + + +
        +

        Mapping Quality

        + + + + + +
        Mean Mapping Quality49.97
        +
        + + +
        +

        Insert size

        + + + + + + + + + + + + + +
        Mean75,226.79
        Standard Deviation2,849,315.96
        P25/Median/P75339 / 427 / 535
        +
        + + +
        +

        Mismatches and indels

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        General error rate1.49%
        Mismatches190,508
        Insertions2,279
        Mapped reads with at least one insertion3.3%
        Deletions2,316
        Mapped reads with at least one deletion3.41%
        Homopolymer indels50.79%
        +
        + + +
        +

        Chromosome stats

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        NameLengthMapped basesMean coverageStandard deviation
        124925062110632020.00430.1147
        224319937310910860.00450.082
        31980224309063020.00460.0765
        41911542768999760.00470.088
        51809152607593180.00420.0739
        61711150677344710.00430.0752
        71591386636541650.00410.0773
        81463640226769340.00460.1184
        91412134315250970.00370.0766
        101355347477247770.00530.1311
        111350065165891180.00440.082
        121338518955812680.00430.0745
        131151698784249150.00370.0689
        141073495403853630.00360.068
        151025313923610060.00350.0671
        16903547534058460.00450.0833
        17811952103513660.00430.0765
        18780772483550350.00450.0817
        19591289832631660.00450.0888
        20630255202628140.00420.0805
        21481298951792590.00370.0748
        22513045661505780.00290.0612
        X1552705606690250.00430.0753
        Y59373566289980.00050.049
        MT16569562513.3952.0903
        GL000207.14262000
        GL000226.115008219531.46281.7817
        GL000229.119913000
        GL000231.12738611690.04270.2278
        GL000210.127682000
        GL000239.133824000
        GL000235.134474000
        GL000201.136148000
        GL000247.136422000
        GL000245.1366514810.01310.1138
        GL000197.137175000
        GL000203.1374984590.01220.1178
        GL000246.138154000
        GL000249.1385024830.01250.1113
        GL000196.138914000
        GL000248.1397864560.01150.1064
        GL000244.139929000
        GL000238.1399394100.01030.1008
        GL000202.1401034230.01050.1417
        GL000234.1405317330.01810.1675
        GL000232.1406525430.01340.1194
        GL000206.141001000
        GL000240.1419334750.01130.1056
        GL000236.1419349240.0220.1466
        GL000241.1421529300.02210.1716
        GL000243.1433411100.00250.0503
        GL000242.1435234440.01020.1005
        GL000230.1436919390.02150.1544
        GL000237.1458678520.01860.135
        GL000233.145941000
        GL000204.18131013450.01650.1549
        GL000198.19008517500.01940.1441
        GL000208.19268939980.04310.2697
        GL000191.1106433000
        GL000227.11283744760.00370.0608
        GL000228.112912043390.03360.3105
        GL000214.113771822200.01610.1342
        GL000221.115539728090.01810.174
        GL000209.11591694630.00290.0574
        GL000218.116114713690.00850.1116
        GL000220.1161802402350.24870.6522
        GL000213.11642394900.0030.0545
        GL000211.11665663840.00230.0679
        GL000199.1169874211540.12450.5192
        GL000217.117214924030.0140.1307
        GL000216.1172294134200.07790.4454
        GL000215.11725459600.00560.0995
        GL000205.117458817780.01020.1251
        GL000219.117919812050.00670.092
        GL000224.117969325230.0140.1396
        GL000223.11804556220.00340.0586
        GL000195.118289621730.01190.1236
        GL000212.118685812740.00680.1243
        GL000222.11868614370.00230.0482
        GL000200.11870353700.0020.0629
        GL000193.118978936420.01920.1547
        GL000194.119146912600.00660.0909
        GL000225.1211173100940.04780.2717
        GL000192.154749634520.00630.0849
        NC_007605171823128640.07490.298
        +
        + +
        +
        + + + +
        + +

        Coverage across reference 

        + +
        + +
        + + +
        + +

        Coverage Histogram 

        + +
        + +
        + + +
        + +

        Coverage Histogram (0-50X) 

        + +
        + +
        + + +
        + +

        Genome Fraction Coverage 

        + +
        + +
        + + +
        + +

        Duplication Rate Histogram 

        + +
        + +
        + + +
        + +

        Mapped Reads Nucleotide Content 

        + +
        + +
        + + +
        + +

        Mapped Reads GC-content Distribution 

        + +
        + +
        + + +
        + +

        Mapped Reads Clipping Profile 

        + +
        + +
        + + +
        + +

        Homopolymer Indels 

        + +
        + +
        + + +
        + +

        Mapping Quality Across Reference 

        + +
        + +
        + + +
        + +

        Mapping Quality Histogram 

        + +
        + +
        + + +
        + +

        Insert Size Across Reference 

        + +
        + +
        + + +
        + +

        Insert Size Histogram 

        + +
        + +
        + + +
        + +
        + +
        + +
        + + +
        +

        Contents

        +
      • Input data & parameters
        • +
      • Summary
        • +
      • Coverage across reference
        • +
      • Coverage Histogram
        • +
      • Coverage Histogram (0-50X)
        • +
      • Genome Fraction Coverage
        • +
      • Duplication Rate Histogram
        • +
      • Mapped Reads Nucleotide Content
        • +
      • Mapped Reads GC-content Distribution
        • +
      • Mapped Reads Clipping Profile
        • +
      • Homopolymer Indels
        • +
      • Mapping Quality Across Reference
        • +
      • Mapping Quality Histogram
        • +
      • Insert Size Across Reference
        • +
      • Insert Size Histogram
        • +
        + +
        +
        + +
        + + +
        +
        +
        +
        +2018/07/26 16:33:36 +
        +
        +
        +
        +Generated by QualiMap v.2.2.2-dev +
        +
        +
        +
        + diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/raw_data_qualimapReport/coverage_across_reference.txt --- /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 0.0036567649377648474 +1.899960795E8 0.0048553554623619365 +1.977510215E8 0.003977850511325552 +2.055059635E8 0.003440902588310783 +2.132609055E8 0.004088618586702519 +2.210158475E8 0.004005832667736264 +2.287707895E8 0.004868508365375266 +2.365257315E8 0.004684109823129561 +2.442806735E8 0.004428272964517336 +2.48704383E8 0.0036513354514557286 +2.52581854E8 0.0037685751444848114 +2.597905575E8 0.004535172539008029 +2.675454995E8 0.004152448851326032 +2.753004415E8 0.0036752047919894177 +2.830553835E8 0.004905259123794865 +2.908103255E8 0.004131043146421985 +2.985652675E8 0.004607513505581344 +3.063202095E8 0.0037604407615169783 +3.140751515E8 0.005089915566099656 +3.218300935E8 0.0036723678913394837 +3.295850355E8 0.004456126170898506 +3.373399775E8 0.005148329929482387 +3.450949195E8 0.008055121495428334 +3.528498615E8 0.0038842327898777323 +3.606048035E8 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+3.0986053035E9 0.1245275910380635 +3.098776315E9 0.013958837983374868 +3.0989485365E9 0.07789011805402393 +3.099120956E9 0.005563765974093715 +3.0992945225E9 0.010183975989185969 +3.0994714155E9 0.006724405406310338 +3.099650861E9 0.014040613713388947 +3.099830935E9 0.0034468427031669946 +3.1000126105E9 0.011881069022832648 +3.1001974875E9 0.006818011538173372 +3.100384347E9 0.0023386367406789004 +3.100571295E9 0.0019782393669634025 +3.100759707E9 0.019189731754738155 +3.100950336E9 0.006580699747739843 +3.101151657E9 0.04779967135950145 +3.1015309915E9 0.006305068895480515 +3.101890651E9 0.07486774180406582 diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/raw_data_qualimapReport/coverage_histogram.txt --- /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 diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/raw_data_qualimapReport/duplication_rate_histogram.txt --- /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 diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/raw_data_qualimapReport/genome_fraction_coverage.txt --- /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 diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/raw_data_qualimapReport/homopolymer_indels.txt --- /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 diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/raw_data_qualimapReport/insert_size_across_reference.txt --- /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 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5.0 +936.0 1.0 +937.0 3.0 +938.0 3.0 +940.0 3.0 +941.0 1.0 +942.0 2.0 +943.0 2.0 +944.0 1.0 +945.0 5.0 +946.0 3.0 +947.0 2.0 +948.0 1.0 +949.0 1.0 +950.0 1.0 +951.0 1.0 +952.0 7.0 +953.0 1.0 +954.0 3.0 +955.0 1.0 +956.0 2.0 +957.0 1.0 +958.0 2.0 +959.0 1.0 +960.0 3.0 +962.0 2.0 +963.0 2.0 +965.0 2.0 +966.0 5.0 +967.0 2.0 +969.0 1.0 +972.0 1.0 +973.0 1.0 +975.0 1.0 +977.0 2.0 +979.0 2.0 +981.0 2.0 +982.0 2.0 +985.0 1.0 +986.0 1.0 +988.0 1.0 +989.0 1.0 +991.0 1.0 +993.0 1.0 +994.0 1.0 +995.0 1.0 +998.0 2.0 +999.0 1.0 +1000.0 2.0 +1001.0 3.0 +1002.0 1.0 +1005.0 1.0 +1006.0 2.0 +1007.0 2.0 +1011.0 2.0 +1012.0 1.0 +1016.0 1.0 +1018.0 2.0 +1019.0 1.0 +1021.0 3.0 +1024.0 1.0 +1025.0 1.0 +1027.0 1.0 +1031.0 1.0 +1034.0 2.0 +1035.0 2.0 +1040.0 1.0 +1041.0 2.0 +1042.0 1.0 +1044.0 1.0 +1045.0 1.0 +1046.0 1.0 +1047.0 1.0 +1048.0 3.0 +1054.0 3.0 +1056.0 1.0 +1062.0 1.0 +1063.0 1.0 +1065.0 1.0 +1067.0 1.0 diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/raw_data_qualimapReport/mapped_reads_clipping_profile.txt --- /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 0.5660542788867227 +32.0 0.5530421787505145 +33.0 0.5386897764543536 +34.0 0.5246724496981807 +35.0 0.5165189448918014 +36.0 0.509594050398712 +37.0 0.4937338081726041 +38.0 0.4768124934032003 +39.0 0.4638562391903234 +40.0 0.4501739879741389 +41.0 0.4374411174545875 +42.0 0.4262719327883143 +43.0 0.4166105880519881 +44.0 0.40683755146899914 +45.0 0.3968411311926846 +46.0 0.385895330219737 +47.0 0.37628983140674205 +48.0 0.3684155562170195 +49.0 0.3597594381006578 +50.0 0.3503773229809884 +51.0 0.3431173529479108 +52.0 0.3361924584548215 +53.0 0.3288766424984126 +54.0 0.3220075939286546 +55.0 0.31541777497555346 +56.0 0.30810195901914456 +57.0 0.30184721560603156 +58.0 0.29475478334294813 +59.0 0.28900265323981744 +60.0 0.2837531364466691 +61.0 0.2786153115001834 +62.0 0.2731424110137096 +63.0 0.26867473714720036 +64.0 0.26303429889073243 +65.0 0.258231549484235 +66.0 0.253652183771063 +67.0 0.2495754313678733 +68.0 0.2462805218913227 +69.0 0.24365576349474855 +70.0 0.23980239478488427 +71.0 0.2350554913017182 +72.0 0.23075535520520304 +73.0 0.22673444872534473 +74.0 0.22371876886545095 +75.0 0.22020047569557494 +76.0 0.21779910099232622 +77.0 0.21562110998240297 +78.0 0.21014820949592913 +79.0 0.20696499186604128 +80.0 0.20383762015948478 +81.0 0.20093363214625376 +82.0 0.19741533897637775 +83.0 0.19367366211317621 +84.0 0.1914398251799216 +85.0 0.1890384504766729 +86.0 0.18635784615676732 +87.0 0.18451493068683225 +88.0 0.1824486315235717 +89.0 0.180661561976968 +90.0 0.177757573963737 +91.0 0.17641727180378425 +92.0 0.175467891107151 +93.0 0.17351328379055322 +94.0 0.17194959793727496 +95.0 0.16977160692735171 +96.0 0.16804038330407936 +97.0 0.16658838929746386 +98.0 0.16496885752085425 +99.0 0.1647454738275288 +100.0 0.16374024720756422 +101.0 0.16223240727761734 +102.0 0.16122718065765276 +103.0 0.15977518665103724 +104.0 0.15876996003107266 +105.0 0.15754134971778264 +106.0 0.15631273940449258 +107.0 0.15536335870785936 +108.0 0.15452566985788888 +109.0 0.15391136470124386 +110.0 0.15346459731459294 +111.0 0.15257106254129107 +112.0 0.1520684492313088 +113.0 0.15178921961465197 +114.0 0.1510632226113442 +115.0 0.1508956848413501 +116.0 0.15067230114802463 +117.0 0.15039307153136783 +118.0 0.14972292045139143 +119.0 0.14922030714140913 +120.0 0.14882938567808957 +121.0 0.14860600198476412 +122.0 0.14882938567808957 +123.0 0.14922030714140913 +124.0 0.14933199898807187 +125.0 0.14905276937141504 +126.0 0.1489410775247523 +127.0 0.14860600198476412 +128.0 0.1489410775247523 +129.0 0.14899692344808368 +130.0 0.14933199898807187 +131.0 0.1492761530647405 +132.0 0.14933199898807187 +133.0 0.15000215006804826 +134.0 0.1502255337613737 +135.0 0.15128660630466967 +136.0 0.15162168184465785 +137.0 0.1522359870013029 +138.0 0.15273860031128517 +139.0 0.15329705954459882 +140.0 0.15446982393455752 +141.0 0.15525166686119662 +142.0 0.15653612309781806 +143.0 0.15798811710443356 +144.0 0.15865826818440995 +145.0 0.1600544162676941 +146.0 0.1614505643509782 +147.0 0.1626233287409369 +148.0 0.1645779360575347 +149.0 0.16569485452416202 +150.0 0.16748192407076573 +151.0 0.167984537380748 +152.0 0.1701066824673399 +153.0 0.17211713570726908 +154.0 0.1734015919438905 +155.0 0.17574712072380785 +156.0 0.17736665250041744 +157.0 0.17960048943367207 +158.0 0.1811641752869503 +159.0 0.18272786114022854 +160.0 0.18496169807348317 +161.0 0.18602277061677913 +162.0 0.18875922086001606 +163.0 0.19054629040661974 +164.0 0.1928918191865371 +165.0 0.19557242350644266 +166.0 0.19808549005635412 +167.0 0.20126870768624197 +168.0 0.20489869270278074 +169.0 0.20769098886934903 +170.0 0.2105391309592487 +171.0 0.21450419151577563 +172.0 0.2187484816889594 +173.0 0.22087062677555136 +174.0 0.2241655362521019 +175.0 0.22690198649533883 +176.0 0.23002935820189532 +177.0 0.2331008839851204 +178.0 0.23656333123166506 +179.0 0.24008162440154113 +180.0 0.2437116094180799 +181.0 0.24773251589793824 +182.0 0.25158588460780246 +183.0 0.25583017478098624 +184.0 0.26063292418748374 +185.0 0.26476552251400476 +186.0 0.26951242599717085 +187.0 0.2737008702470233 +188.0 0.27766593080355023 +189.0 0.2822452965167222 +190.0 0.2868246622298942 +191.0 0.29285602194968174 +192.0 0.29927830313278875 +193.0 0.3048628954659253 +194.0 0.3120670195756715 +195.0 0.31932698960874906 +196.0 0.3258609626385188 +197.0 0.33189232235830635 +198.0 0.33965490570136614 +199.0 0.34635641650113 +200.0 0.35506838054082307 +201.0 0.36361280681052205 +202.0 0.3729949219301915 +203.0 0.3826004207431864 +204.0 0.3922617654795127 +205.0 0.4024815694491526 +206.0 0.41136107125883975 +207.0 0.4214691833818169 +208.0 0.4325825221247586 +209.0 0.4457621600309609 +210.0 0.4572664202372223 +211.0 0.47122790107006374 +212.0 0.48893105876610665 +213.0 0.5046796091455518 +214.0 0.5125538843352744 +215.0 0.5206515432183224 +216.0 0.5357857884411225 +217.0 0.5501381907372834 +218.0 0.5643230552634503 +219.0 0.5817469833428364 +220.0 0.5972163041056248 +221.0 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 diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt --- /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 diff -r 71af3fbe85be -r 418ee04dd1b2 test-data/test_stats/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt --- /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 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