changeset 30:418ee04dd1b2 draft

planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
author scottx611x
date Thu, 26 Jul 2018 16:40:19 -0400
parents 71af3fbe85be
children a77bae54b1c7
files qualimap_bamqc.py test-data/test_stats/css/agogo.css test-data/test_stats/css/ajax-loader.gif test-data/test_stats/css/basic.css test-data/test_stats/css/bgfooter.png test-data/test_stats/css/bgtop.png test-data/test_stats/css/comment-bright.png test-data/test_stats/css/comment-close.png test-data/test_stats/css/comment.png test-data/test_stats/css/doctools.js test-data/test_stats/css/down-pressed.png test-data/test_stats/css/down.png test-data/test_stats/css/file.png test-data/test_stats/css/jquery.js test-data/test_stats/css/minus.png test-data/test_stats/css/plus.png test-data/test_stats/css/pygments.css test-data/test_stats/css/qualimap_logo_small.png test-data/test_stats/css/report.css test-data/test_stats/css/searchtools.js test-data/test_stats/css/underscore.js test-data/test_stats/css/up-pressed.png test-data/test_stats/css/up.png test-data/test_stats/css/websupport.js test-data/test_stats/genome_results.txt test-data/test_stats/images_qualimapReport/genome_coverage_0to50_histogram.png test-data/test_stats/images_qualimapReport/genome_coverage_across_reference.png test-data/test_stats/images_qualimapReport/genome_coverage_histogram.png test-data/test_stats/images_qualimapReport/genome_coverage_quotes.png test-data/test_stats/images_qualimapReport/genome_gc_content_per_window.png test-data/test_stats/images_qualimapReport/genome_homopolymer_indels.png test-data/test_stats/images_qualimapReport/genome_insert_size_across_reference.png test-data/test_stats/images_qualimapReport/genome_insert_size_histogram.png test-data/test_stats/images_qualimapReport/genome_mapping_quality_across_reference.png test-data/test_stats/images_qualimapReport/genome_mapping_quality_histogram.png test-data/test_stats/images_qualimapReport/genome_reads_clipping_profile.png test-data/test_stats/images_qualimapReport/genome_reads_content_per_read_position.png test-data/test_stats/images_qualimapReport/genome_uniq_read_starts_histogram.png test-data/test_stats/qualimapReport.html test-data/test_stats/raw_data_qualimapReport/coverage_across_reference.txt test-data/test_stats/raw_data_qualimapReport/coverage_histogram.txt test-data/test_stats/raw_data_qualimapReport/duplication_rate_histogram.txt test-data/test_stats/raw_data_qualimapReport/genome_fraction_coverage.txt test-data/test_stats/raw_data_qualimapReport/homopolymer_indels.txt test-data/test_stats/raw_data_qualimapReport/insert_size_across_reference.txt test-data/test_stats/raw_data_qualimapReport/insert_size_histogram.txt test-data/test_stats/raw_data_qualimapReport/mapped_reads_clipping_profile.txt test-data/test_stats/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt test-data/test_stats/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt test-data/test_stats/raw_data_qualimapReport/mapping_quality_across_reference.txt test-data/test_stats/raw_data_qualimapReport/mapping_quality_histogram.txt
diffstat 51 files changed, 7482 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/qualimap_bamqc.py	Thu Jul 26 16:21:44 2018 -0400
+++ b/qualimap_bamqc.py	Thu Jul 26 16:40:19 2018 -0400
@@ -2,17 +2,18 @@
 from __future__ import print_function
 import argparse
 from subprocess import check_call, CalledProcessError
-import os
 import shutil
 import sys
 
+OUTPUT_DIR = "qualimap_results"
+
 
 def qualimap_bamqc(bam_filename, genomecov_file, jv_mem_size):
     qualimap_command = [
         "qualimap", "bamqc",
         "-bam " + bam_filename,
         "-oc " + genomecov_file,
-        "-outdir .",
+        "-outdir " + OUTPUT_DIR,
         "--java-mem-size=" + jv_mem_size
     ]
 
@@ -38,12 +39,12 @@
         args.java_mem_size
     )
 
-    print(os.listdir("../"))
-
+    shutil.move(OUTPUT_DIR + "/genome_results.txt", "genome_results.txt")
+    shutil.move(OUTPUT_DIR + "/qualimapReport.html", "qualimapReport.html")
     shutil.make_archive(
         'raw_data_qualimapReport',
         'zip',
-        os.path.join("../", 'raw_data_qualimapReport')
+        OUTPUT_DIR + '/raw_data_qualimapReport'
     )
 
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/css/agogo.css	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,471 @@
+/*
+ * agogo.css_t
+ * ~~~~~~~~~~~
+ *
+ * Sphinx stylesheet -- agogo theme.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+* {
+  margin: 0px;
+  padding: 0px;
+}
+
+body {
+  font-family: "Verdana", Arial, sans-serif;
+  line-height: 1.4em;
+  color: black;
+  background-color: #eeeeec;
+}
+
+
+/* Page layout */
+
+div.header, div.content, div.footer {
+  width: 70em;
+  margin-left: auto;
+  margin-right: auto;
+}
+
+div.header-wrapper {
+  background: url(bgtop.png) top left repeat-x;
+  border-bottom: 3px solid #2e3436;
+}
+
+
+/* Default body styles */
+a {
+  color: #ce5c00;
+}
+
+div.bodywrapper a, div.footer a {
+  text-decoration: underline;
+}
+
+.clearer {
+  clear: both;
+}
+
+.left {
+  float: left;
+}
+
+.right {
+  float: right;
+}
+
+.line-block {
+    display: block;
+    margin-top: 1em;
+    margin-bottom: 1em;
+}
+
+.line-block .line-block {
+    margin-top: 0;
+    margin-bottom: 0;
+    margin-left: 1.5em;
+}
+
+h1, h2, h3, h4 {
+  font-family: "Georgia", "Times New Roman", serif;
+  font-weight: normal;
+  color: #3465a4;
+  margin-bottom: .8em;
+}
+
+h1 {
+  color: #204a87;
+}
+
+h2 {
+  padding-bottom: .5em;
+  border-bottom: 1px solid #3465a4;
+}
+
+a.headerlink {
+  visibility: hidden;
+  color: #dddddd;
+  padding-left: .3em;
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
+h3:hover > a.headerlink,
+h4:hover > a.headerlink,
+h5:hover > a.headerlink,
+h6:hover > a.headerlink,
+dt:hover > a.headerlink {
+  visibility: visible;
+}
+
+img {
+  border: 0;
+}
+
+div.admonition {
+  margin-top: 10px;
+  margin-bottom: 10px;
+  padding: 2px 7px 1px 7px;
+  border-left: 0.2em solid black;
+}
+
+p.admonition-title {
+  margin: 0px 10px 5px 0px;
+  font-weight: bold;
+}
+
+dt:target, .highlighted {
+  background-color: #fbe54e;
+}
+
+/* Header */
+
+div.header {
+  padding-top: 10px;
+  padding-bottom: 10px;
+}
+
+div.header .headertitle {
+  font-family: "Georgia", "Times New Roman", serif;
+  font-weight: normal;
+  font-size: 180%;
+  letter-spacing: .08em;
+  margin-bottom: .8em;
+}
+
+div.header .headertitle a {
+  color: white;
+}
+
+div.header div.rel {
+  margin-top: 1em;
+}
+
+div.header div.rel a {
+  color: #fcaf3e;
+  letter-spacing: .1em;
+  text-transform: uppercase;
+}
+
+p.logo {
+    float: right;
+}
+
+img.logo {
+    border: 0;
+}
+
+
+/* Content */
+div.content-wrapper {
+  background-color: white;
+  padding-top: 20px;
+  padding-bottom: 20px;
+}
+
+div.document {
+  width: 50em;
+  float: left;
+}
+
+div.body {
+  padding-right: 2em;
+  text-align: justify;
+}
+
+div.document h1 {
+  line-height: 120%;
+}
+
+div.document ul {
+  margin: 1.5em;
+  list-style-type: square;
+}
+
+div.document dd {
+  margin-left: 1.2em;
+  margin-top: .4em;
+  margin-bottom: 1em;
+}
+
+div.document .section {
+  margin-top: 1.7em;
+}
+div.document .section:first-child {
+  margin-top: 0px;
+}
+
+div.document div.highlight {
+  padding: 3px;
+  background-color: #eeeeec;
+  border-top: 2px solid #dddddd;
+  border-bottom: 2px solid #dddddd;
+  margin-top: .8em;
+  margin-bottom: .8em;
+}
+
+div.document h2 {
+  margin-top: .7em;
+}
+
+div.document p {
+  margin-bottom: .5em;
+}
+
+div.document li.toctree-l1 {
+  margin-bottom: 1em;
+}
+
+div.document .descname {
+  font-weight: bold;
+}
+
+div.document .docutils.literal {
+  background-color: #eeeeec;
+  padding: 1px;
+}
+
+div.document .docutils.xref.literal {
+  background-color: transparent;
+  padding: 0px;
+}
+
+div.document blockquote {
+  margin: 1em;
+}
+
+div.document ol {
+  margin: 1.5em;
+}
+
+
+/* Sidebar */
+
+div.sidebar {
+  width: 20em;
+  float: right;
+  font-size: .9em;
+}
+
+div.sidebar a, div.header a {
+  text-decoration: none;
+}
+
+div.sidebar a:hover, div.header a:hover {
+  text-decoration: underline;
+}
+
+div.sidebar h3 {
+  color: #2e3436;
+  text-transform: uppercase;
+  font-size: 130%;
+  letter-spacing: .1em;
+}
+
+div.sidebar ul {
+  list-style-type: none;
+}
+
+div.sidebar li.toctree-l1 a {
+  display: block;
+  padding: 1px;
+  border: 1px solid #dddddd;
+  background-color: #eeeeec;
+  margin-bottom: .4em;
+  padding-left: 3px;
+  color: #2e3436;
+}
+
+div.sidebar li.toctree-l2 a {
+  background-color: transparent;
+  border: none;
+  margin-left: 1em;
+  border-bottom: 1px solid #dddddd;
+}
+
+div.sidebar li.toctree-l3 a {
+  background-color: transparent;
+  border: none;
+  margin-left: 2em;
+  border-bottom: 1px solid #dddddd;
+}
+
+div.sidebar li.toctree-l2:last-child a {
+  border-bottom: none;
+}
+
+div.sidebar li.toctree-l1.current a {
+  border-right: 5px solid #fcaf3e;
+}
+
+div.sidebar li.toctree-l1.current li.toctree-l2 a {
+  border-right: none;
+}
+
+div.sidebar input[type="text"] {
+  width: 170px;
+}
+
+div.sidebar input[type="submit"] {
+  width: 30px;
+}
+
+
+/* Footer */
+
+div.footer-wrapper {
+  background: url(bgfooter.png) top left repeat-x;
+  border-top: 4px solid #babdb6;
+  padding-top: 10px;
+  padding-bottom: 10px;
+  min-height: 80px;
+}
+
+div.footer, div.footer a {
+  color: #888a85;
+}
+
+div.footer .right {
+  text-align: right;
+}
+
+div.footer .left {
+  text-transform: uppercase;
+}
+
+
+/* Styles copied from basic theme */
+
+img.align-left, .figure.align-left, object.align-left {
+    clear: left;
+    float: left;
+    margin-right: 1em;
+}
+
+img.align-right, .figure.align-right, object.align-right {
+    clear: right;
+    float: right;
+    margin-left: 1em;
+}
+
+img.align-center, .figure.align-center, object.align-center {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+}
+
+img.align-center-qualimap {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+  width: 100%
+}
+
+.align-left {
+    text-align: left;
+}
+
+.align-center {
+    text-align: center;
+}
+
+.align-right {
+    text-align: right;
+}
+
+/* -- search page ----------------------------------------------------------- */
+
+ul.search {
+    margin: 10px 0 0 20px;
+    padding: 0;
+}
+
+ul.search li {
+    padding: 5px 0 5px 20px;
+    background-image: url(file.png);
+    background-repeat: no-repeat;
+    background-position: 0 7px;
+}
+
+ul.search li a {
+    font-weight: bold;
+}
+
+ul.search li div.context {
+    color: #888;
+    margin: 2px 0 0 30px;
+    text-align: left;
+}
+
+ul.keywordmatches li.goodmatch a {
+    font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
+    width: 90%;
+}
+
+table.contentstable p.biglink {
+    line-height: 150%;
+}
+
+a.biglink {
+    font-size: 1.3em;
+}
+
+span.linkdescr {
+    font-style: italic;
+    padding-top: 5px;
+    font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable td {
+    text-align: left;
+    vertical-align: top;
+}
+
+table.indextable dl, table.indextable dd {
+    margin-top: 0;
+    margin-bottom: 0;
+}
+
+table.indextable tr.pcap {
+    height: 10px;
+}
+
+table.indextable tr.cap {
+    margin-top: 10px;
+    background-color: #f2f2f2;
+}
+
+img.toggler {
+    margin-right: 3px;
+    margin-top: 3px;
+    cursor: pointer;
+}
+
+/* -- viewcode extension ---------------------------------------------------- */
+
+.viewcode-link {
+    float: right;
+}
+
+.viewcode-back {
+    float: right;
+    font-family:: "Verdana", Arial, sans-serif;
+}
+
+div.viewcode-block:target {
+    margin: -1px -3px;
+    padding: 0 3px;
+    background-color: #f4debf;
+    border-top: 1px solid #ac9;
+    border-bottom: 1px solid #ac9;
+}
Binary file test-data/test_stats/css/ajax-loader.gif has changed
--- /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
Binary file test-data/test_stats/css/bgfooter.png has changed
Binary file test-data/test_stats/css/bgtop.png has changed
Binary file test-data/test_stats/css/comment-bright.png has changed
Binary file test-data/test_stats/css/comment-close.png has changed
Binary file test-data/test_stats/css/comment.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/css/doctools.js	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,247 @@
+/*
+ * doctools.js
+ * ~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for all documentation.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+/**
+ * make the code below compatible with browsers without
+ * an installed firebug like debugger
+if (!window.console || !console.firebug) {
+  var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
+    "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
+    "profile", "profileEnd"];
+  window.console = {};
+  for (var i = 0; i < names.length; ++i)
+    window.console[names[i]] = function() {};
+}
+ */
+
+/**
+ * small helper function to urldecode strings
+ */
+jQuery.urldecode = function(x) {
+  return decodeURIComponent(x).replace(/\+/g, ' ');
+}
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+  if (typeof s == 'undefined')
+    s = document.location.search;
+  var parts = s.substr(s.indexOf('?') + 1).split('&');
+  var result = {};
+  for (var i = 0; i < parts.length; i++) {
+    var tmp = parts[i].split('=', 2);
+    var key = jQuery.urldecode(tmp[0]);
+    var value = jQuery.urldecode(tmp[1]);
+    if (key in result)
+      result[key].push(value);
+    else
+      result[key] = [value];
+  }
+  return result;
+};
+
+/**
+ * small function to check if an array contains
+ * a given item.
+ */
+jQuery.contains = function(arr, item) {
+  for (var i = 0; i < arr.length; i++) {
+    if (arr[i] == item)
+      return true;
+  }
+  return false;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+  function highlight(node) {
+    if (node.nodeType == 3) {
+      var val = node.nodeValue;
+      var pos = val.toLowerCase().indexOf(text);
+      if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) {
+        var span = document.createElement("span");
+        span.className = className;
+        span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+        node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+          document.createTextNode(val.substr(pos + text.length)),
+          node.nextSibling));
+        node.nodeValue = val.substr(0, pos);
+      }
+    }
+    else if (!jQuery(node).is("button, select, textarea")) {
+      jQuery.each(node.childNodes, function() {
+        highlight(this);
+      });
+    }
+  }
+  return this.each(function() {
+    highlight(this);
+  });
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+var Documentation = {
+
+  init : function() {
+    this.fixFirefoxAnchorBug();
+    this.highlightSearchWords();
+    this.initIndexTable();
+  },
+
+  /**
+   * i18n support
+   */
+  TRANSLATIONS : {},
+  PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
+  LOCALE : 'unknown',
+
+  // gettext and ngettext don't access this so that the functions
+  // can safely bound to a different name (_ = Documentation.gettext)
+  gettext : function(string) {
+    var translated = Documentation.TRANSLATIONS[string];
+    if (typeof translated == 'undefined')
+      return string;
+    return (typeof translated == 'string') ? translated : translated[0];
+  },
+
+  ngettext : function(singular, plural, n) {
+    var translated = Documentation.TRANSLATIONS[singular];
+    if (typeof translated == 'undefined')
+      return (n == 1) ? singular : plural;
+    return translated[Documentation.PLURALEXPR(n)];
+  },
+
+  addTranslations : function(catalog) {
+    for (var key in catalog.messages)
+      this.TRANSLATIONS[key] = catalog.messages[key];
+    this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
+    this.LOCALE = catalog.locale;
+  },
+
+  /**
+   * add context elements like header anchor links
+   */
+  addContextElements : function() {
+    $('div[id] > :header:first').each(function() {
+      $('<a class="headerlink">\u00B6</a>').
+      attr('href', '#' + this.id).
+      attr('title', _('Permalink to this headline')).
+      appendTo(this);
+    });
+    $('dt[id]').each(function() {
+      $('<a class="headerlink">\u00B6</a>').
+      attr('href', '#' + this.id).
+      attr('title', _('Permalink to this definition')).
+      appendTo(this);
+    });
+  },
+
+  /**
+   * workaround a firefox stupidity
+   */
+  fixFirefoxAnchorBug : function() {
+    if (document.location.hash && $.browser.mozilla)
+      window.setTimeout(function() {
+        document.location.href += '';
+      }, 10);
+  },
+
+  /**
+   * highlight the search words provided in the url in the text
+   */
+  highlightSearchWords : function() {
+    var params = $.getQueryParameters();
+    var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
+    if (terms.length) {
+      var body = $('div.body');
+      window.setTimeout(function() {
+        $.each(terms, function() {
+          body.highlightText(this.toLowerCase(), 'highlighted');
+        });
+      }, 10);
+      $('<p class="highlight-link"><a href="javascript:Documentation.' +
+        'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
+          .appendTo($('#searchbox'));
+    }
+  },
+
+  /**
+   * init the domain index toggle buttons
+   */
+  initIndexTable : function() {
+    var togglers = $('img.toggler').click(function() {
+      var src = $(this).attr('src');
+      var idnum = $(this).attr('id').substr(7);
+      $('tr.cg-' + idnum).toggle();
+      if (src.substr(-9) == 'minus.png')
+        $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
+      else
+        $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
+    }).css('display', '');
+    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
+        togglers.click();
+    }
+  },
+
+  /**
+   * helper function to hide the search marks again
+   */
+  hideSearchWords : function() {
+    $('#searchbox .highlight-link').fadeOut(300);
+    $('span.highlighted').removeClass('highlighted');
+  },
+
+  /**
+   * make the url absolute
+   */
+  makeURL : function(relativeURL) {
+    return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
+  },
+
+  /**
+   * get the current relative url
+   */
+  getCurrentURL : function() {
+    var path = document.location.pathname;
+    var parts = path.split(/\//);
+    $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
+      if (this == '..')
+        parts.pop();
+    });
+    var url = parts.join('/');
+    return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+  }
+};
+
+// quick alias for translations
+_ = Documentation.gettext;
+
+$(document).ready(function() {
+  Documentation.init();
+});
Binary file test-data/test_stats/css/down-pressed.png has changed
Binary file test-data/test_stats/css/down.png has changed
Binary file test-data/test_stats/css/file.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/css/jquery.js	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,154 @@
+/*!
+ * jQuery JavaScript Library v1.4.2
+ * http://jquery.com/
+ *
+ * Copyright 2010, John Resig
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * Includes Sizzle.js
+ * http://sizzlejs.com/
+ * Copyright 2010, The Dojo Foundation
+ * Released under the MIT, BSD, and GPL Licenses.
+ *
+ * Date: Sat Feb 13 22:33:48 2010 -0500
+ */
+(function(A,w){function ma(){if(!c.isReady){try{s.documentElement.doScroll("left")}catch(a){setTimeout(ma,1);return}c.ready()}}function Qa(a,b){b.src?c.ajax({url:b.src,async:false,dataType:"script"}):c.globalEval(b.text||b.textContent||b.innerHTML||"");b.parentNode&&b.parentNode.removeChild(b)}function X(a,b,d,f,e,j){var i=a.length;if(typeof b==="object"){for(var o in b)X(a,o,b[o],f,e,d);return a}if(d!==w){f=!j&&f&&c.isFunction(d);for(o=0;o<i;o++)e(a[o],b,f?d.call(a[o],o,e(a[o],b)):d,j);return a}return i?
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+f.position==="fixed"){k+=Math.max(i.scrollTop,o.scrollTop);n+=Math.max(i.scrollLeft,o.scrollLeft)}return{top:k,left:n}};c.offset={initialize:function(){var a=s.body,b=s.createElement("div"),d,f,e,j=parseFloat(c.curCSS(a,"marginTop",true))||0;c.extend(b.style,{position:"absolute",top:0,left:0,margin:0,border:0,width:"1px",height:"1px",visibility:"hidden"});b.innerHTML="<div style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;'><div></div></div><table style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;' cellpadding='0' cellspacing='0'><tr><td></td></tr></table>";
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+d,e);d={top:b.top-e.top+j,left:b.left-e.left+i};"using"in b?b.using.call(a,d):f.css(d)}};c.fn.extend({position:function(){if(!this[0])return null;var a=this[0],b=this.offsetParent(),d=this.offset(),f=/^body|html$/i.test(b[0].nodeName)?{top:0,left:0}:b.offset();d.top-=parseFloat(c.curCSS(a,"marginTop",true))||0;d.left-=parseFloat(c.curCSS(a,"marginLeft",true))||0;f.top+=parseFloat(c.curCSS(b[0],"borderTopWidth",true))||0;f.left+=parseFloat(c.curCSS(b[0],"borderLeftWidth",true))||0;return{top:d.top-
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Binary file test-data/test_stats/css/minus.png has changed
Binary file test-data/test_stats/css/plus.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/css/pygments.css	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,62 @@
+.highlight .hll { background-color: #ffffcc }
+.highlight  { background: #eeffcc; }
+.highlight .c { color: #408090; font-style: italic } /* Comment */
+.highlight .err { border: 1px solid #FF0000 } /* Error */
+.highlight .k { color: #007020; font-weight: bold } /* Keyword */
+.highlight .o { color: #666666 } /* Operator */
+.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #007020 } /* Comment.Preproc */
+.highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
+.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
+.highlight .gd { color: #A00000 } /* Generic.Deleted */
+.highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .gr { color: #FF0000 } /* Generic.Error */
+.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
+.highlight .gi { color: #00A000 } /* Generic.Inserted */
+.highlight .go { color: #303030 } /* Generic.Output */
+.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
+.highlight .gs { font-weight: bold } /* Generic.Strong */
+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #0040D0 } /* Generic.Traceback */
+.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #007020 } /* Keyword.Pseudo */
+.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
+.highlight .kt { color: #902000 } /* Keyword.Type */
+.highlight .m { color: #208050 } /* Literal.Number */
+.highlight .s { color: #4070a0 } /* Literal.String */
+.highlight .na { color: #4070a0 } /* Name.Attribute */
+.highlight .nb { color: #007020 } /* Name.Builtin */
+.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */
+.highlight .no { color: #60add5 } /* Name.Constant */
+.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */
+.highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */
+.highlight .ne { color: #007020 } /* Name.Exception */
+.highlight .nf { color: #06287e } /* Name.Function */
+.highlight .nl { color: #002070; font-weight: bold } /* Name.Label */
+.highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */
+.highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */
+.highlight .nv { color: #bb60d5 } /* Name.Variable */
+.highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
+.highlight .w { color: #bbbbbb } /* Text.Whitespace */
+.highlight .mf { color: #208050 } /* Literal.Number.Float */
+.highlight .mh { color: #208050 } /* Literal.Number.Hex */
+.highlight .mi { color: #208050 } /* Literal.Number.Integer */
+.highlight .mo { color: #208050 } /* Literal.Number.Oct */
+.highlight .sb { color: #4070a0 } /* Literal.String.Backtick */
+.highlight .sc { color: #4070a0 } /* Literal.String.Char */
+.highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */
+.highlight .s2 { color: #4070a0 } /* Literal.String.Double */
+.highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
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+.highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */
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+.highlight .sr { color: #235388 } /* Literal.String.Regex */
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+.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
Binary file test-data/test_stats/css/qualimap_logo_small.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/css/report.css	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,50 @@
+div.summary{
+
+}
+
+table.summary{
+
+	border: 0px;
+  width: 100%;
+  vertical-align: top;
+
+}
+
+div.table-summary{
+	margin-left:auto; 
+  margin-right:auto; 
+	padding-bottom: 20px;
+}
+
+td.column1{
+	width: 60%;
+}
+
+table.hovertable {
+
+	font-size:14px;
+
+	border-width: 1px;
+	border-color: #999999;
+	border-collapse: collapse;
+}
+table.hovertable th {
+	background-color:#FFFFFF;
+	border-width: 1px;
+	padding: 8px;
+	border-style: solid;
+	border-color: #a9c6c9;
+}
+table.hovertable tr {
+	background-color:#FFFFFF;
+}
+table.hovertable td {
+	border-width: 1px;
+	padding: 8px;
+	border-style: solid;
+	border-color: #a9c6c9;
+}
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/css/searchtools.js	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,560 @@
+/*
+ * searchtools.js_t
+ * ~~~~~~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilties for the full-text search.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * helper function to return a node containing the
+ * search summary for a given text. keywords is a list
+ * of stemmed words, hlwords is the list of normal, unstemmed
+ * words. the first one is used to find the occurance, the
+ * latter for highlighting it.
+ */
+
+jQuery.makeSearchSummary = function(text, keywords, hlwords) {
+  var textLower = text.toLowerCase();
+  var start = 0;
+  $.each(keywords, function() {
+    var i = textLower.indexOf(this.toLowerCase());
+    if (i > -1)
+      start = i;
+  });
+  start = Math.max(start - 120, 0);
+  var excerpt = ((start > 0) ? '...' : '') +
+  $.trim(text.substr(start, 240)) +
+  ((start + 240 - text.length) ? '...' : '');
+  var rv = $('<div class="context"></div>').text(excerpt);
+  $.each(hlwords, function() {
+    rv = rv.highlightText(this, 'highlighted');
+  });
+  return rv;
+}
+
+
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+  var step2list = {
+    ational: 'ate',
+    tional: 'tion',
+    enci: 'ence',
+    anci: 'ance',
+    izer: 'ize',
+    bli: 'ble',
+    alli: 'al',
+    entli: 'ent',
+    eli: 'e',
+    ousli: 'ous',
+    ization: 'ize',
+    ation: 'ate',
+    ator: 'ate',
+    alism: 'al',
+    iveness: 'ive',
+    fulness: 'ful',
+    ousness: 'ous',
+    aliti: 'al',
+    iviti: 'ive',
+    biliti: 'ble',
+    logi: 'log'
+  };
+
+  var step3list = {
+    icate: 'ic',
+    ative: '',
+    alize: 'al',
+    iciti: 'ic',
+    ical: 'ic',
+    ful: '',
+    ness: ''
+  };
+
+  var c = "[^aeiou]";          // consonant
+  var v = "[aeiouy]";          // vowel
+  var C = c + "[^aeiouy]*";    // consonant sequence
+  var V = v + "[aeiou]*";      // vowel sequence
+
+  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
+  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
+  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
+  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
+
+  this.stemWord = function (w) {
+    var stem;
+    var suffix;
+    var firstch;
+    var origword = w;
+
+    if (w.length < 3)
+      return w;
+
+    var re;
+    var re2;
+    var re3;
+    var re4;
+
+    firstch = w.substr(0,1);
+    if (firstch == "y")
+      w = firstch.toUpperCase() + w.substr(1);
+
+    // Step 1a
+    re = /^(.+?)(ss|i)es$/;
+    re2 = /^(.+?)([^s])s$/;
+
+    if (re.test(w))
+      w = w.replace(re,"$1$2");
+    else if (re2.test(w))
+      w = w.replace(re2,"$1$2");
+
+    // Step 1b
+    re = /^(.+?)eed$/;
+    re2 = /^(.+?)(ed|ing)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = new RegExp(mgr0);
+      if (re.test(fp[1])) {
+        re = /.$/;
+        w = w.replace(re,"");
+      }
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = new RegExp(s_v);
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = /(at|bl|iz)$/;
+        re3 = new RegExp("([^aeiouylsz])\\1$");
+        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+        if (re2.test(w))
+          w = w + "e";
+        else if (re3.test(w)) {
+          re = /.$/;
+          w = w.replace(re,"");
+        }
+        else if (re4.test(w))
+          w = w + "e";
+      }
+    }
+
+    // Step 1c
+    re = /^(.+?)y$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(s_v);
+      if (re.test(stem))
+        w = stem + "i";
+    }
+
+    // Step 2
+    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step2list[suffix];
+    }
+
+    // Step 3
+    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step3list[suffix];
+    }
+
+    // Step 4
+    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+    re2 = /^(.+?)(s|t)(ion)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      if (re.test(stem))
+        w = stem;
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = new RegExp(mgr1);
+      if (re2.test(stem))
+        w = stem;
+    }
+
+    // Step 5
+    re = /^(.+?)e$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      re2 = new RegExp(meq1);
+      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+        w = stem;
+    }
+    re = /ll$/;
+    re2 = new RegExp(mgr1);
+    if (re.test(w) && re2.test(w)) {
+      re = /.$/;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+    if (firstch == "y")
+      w = firstch.toLowerCase() + w.substr(1);
+    return w;
+  }
+}
+
+
+/**
+ * Search Module
+ */
+var Search = {
+
+  _index : null,
+  _queued_query : null,
+  _pulse_status : -1,
+
+  init : function() {
+      var params = $.getQueryParameters();
+      if (params.q) {
+          var query = params.q[0];
+          $('input[name="q"]')[0].value = query;
+          this.performSearch(query);
+      }
+  },
+
+  loadIndex : function(url) {
+    $.ajax({type: "GET", url: url, data: null, success: null,
+            dataType: "script", cache: true});
+  },
+
+  setIndex : function(index) {
+    var q;
+    this._index = index;
+    if ((q = this._queued_query) !== null) {
+      this._queued_query = null;
+      Search.query(q);
+    }
+  },
+
+  hasIndex : function() {
+      return this._index !== null;
+  },
+
+  deferQuery : function(query) {
+      this._queued_query = query;
+  },
+
+  stopPulse : function() {
+      this._pulse_status = 0;
+  },
+
+  startPulse : function() {
+    if (this._pulse_status >= 0)
+        return;
+    function pulse() {
+      Search._pulse_status = (Search._pulse_status + 1) % 4;
+      var dotString = '';
+      for (var i = 0; i < Search._pulse_status; i++)
+        dotString += '.';
+      Search.dots.text(dotString);
+      if (Search._pulse_status > -1)
+        window.setTimeout(pulse, 500);
+    };
+    pulse();
+  },
+
+  /**
+   * perform a search for something
+   */
+  performSearch : function(query) {
+    // create the required interface elements
+    this.out = $('#search-results');
+    this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
+    this.dots = $('<span></span>').appendTo(this.title);
+    this.status = $('<p style="display: none"></p>').appendTo(this.out);
+    this.output = $('<ul class="search"/>').appendTo(this.out);
+
+    $('#search-progress').text(_('Preparing search...'));
+    this.startPulse();
+
+    // index already loaded, the browser was quick!
+    if (this.hasIndex())
+      this.query(query);
+    else
+      this.deferQuery(query);
+  },
+
+  query : function(query) {
+    var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"];
+
+    // Stem the searchterms and add them to the correct list
+    var stemmer = new Stemmer();
+    var searchterms = [];
+    var excluded = [];
+    var hlterms = [];
+    var tmp = query.split(/\s+/);
+    var objectterms = [];
+    for (var i = 0; i < tmp.length; i++) {
+      if (tmp[i] != "") {
+          objectterms.push(tmp[i].toLowerCase());
+      }
+
+      if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
+          tmp[i] == "") {
+        // skip this "word"
+        continue;
+      }
+      // stem the word
+      var word = stemmer.stemWord(tmp[i]).toLowerCase();
+      // select the correct list
+      if (word[0] == '-') {
+        var toAppend = excluded;
+        word = word.substr(1);
+      }
+      else {
+        var toAppend = searchterms;
+        hlterms.push(tmp[i].toLowerCase());
+      }
+      // only add if not already in the list
+      if (!$.contains(toAppend, word))
+        toAppend.push(word);
+    };
+    var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
+
+    // console.debug('SEARCH: searching for:');
+    // console.info('required: ', searchterms);
+    // console.info('excluded: ', excluded);
+
+    // prepare search
+    var filenames = this._index.filenames;
+    var titles = this._index.titles;
+    var terms = this._index.terms;
+    var fileMap = {};
+    var files = null;
+    // different result priorities
+    var importantResults = [];
+    var objectResults = [];
+    var regularResults = [];
+    var unimportantResults = [];
+    $('#search-progress').empty();
+
+    // lookup as object
+    for (var i = 0; i < objectterms.length; i++) {
+      var others = [].concat(objectterms.slice(0,i),
+                             objectterms.slice(i+1, objectterms.length))
+      var results = this.performObjectSearch(objectterms[i], others);
+      // Assume first word is most likely to be the object,
+      // other words more likely to be in description.
+      // Therefore put matches for earlier words first.
+      // (Results are eventually used in reverse order).
+      objectResults = results[0].concat(objectResults);
+      importantResults = results[1].concat(importantResults);
+      unimportantResults = results[2].concat(unimportantResults);
+    }
+
+    // perform the search on the required terms
+    for (var i = 0; i < searchterms.length; i++) {
+      var word = searchterms[i];
+      // no match but word was a required one
+      if ((files = terms[word]) == null)
+        break;
+      if (files.length == undefined) {
+        files = [files];
+      }
+      // create the mapping
+      for (var j = 0; j < files.length; j++) {
+        var file = files[j];
+        if (file in fileMap)
+          fileMap[file].push(word);
+        else
+          fileMap[file] = [word];
+      }
+    }
+
+    // now check if the files don't contain excluded terms
+    for (var file in fileMap) {
+      var valid = true;
+
+      // check if all requirements are matched
+      if (fileMap[file].length != searchterms.length)
+        continue;
+
+      // ensure that none of the excluded terms is in the
+      // search result.
+      for (var i = 0; i < excluded.length; i++) {
+        if (terms[excluded[i]] == file ||
+            $.contains(terms[excluded[i]] || [], file)) {
+          valid = false;
+          break;
+        }
+      }
+
+      // if we have still a valid result we can add it
+      // to the result list
+      if (valid)
+        regularResults.push([filenames[file], titles[file], '', null]);
+    }
+
+    // delete unused variables in order to not waste
+    // memory until list is retrieved completely
+    delete filenames, titles, terms;
+
+    // now sort the regular results descending by title
+    regularResults.sort(function(a, b) {
+      var left = a[1].toLowerCase();
+      var right = b[1].toLowerCase();
+      return (left > right) ? -1 : ((left < right) ? 1 : 0);
+    });
+
+    // combine all results
+    var results = unimportantResults.concat(regularResults)
+      .concat(objectResults).concat(importantResults);
+
+    // print the results
+    var resultCount = results.length;
+    function displayNextItem() {
+      // results left, load the summary and display it
+      if (results.length) {
+        var item = results.pop();
+        var listItem = $('<li style="display:none"></li>');
+        if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') {
+          // dirhtml builder
+          var dirname = item[0] + '/';
+          if (dirname.match(/\/index\/$/)) {
+            dirname = dirname.substring(0, dirname.length-6);
+          } else if (dirname == 'index/') {
+            dirname = '';
+          }
+          listItem.append($('<a/>').attr('href',
+            DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
+            highlightstring + item[2]).html(item[1]));
+        } else {
+          // normal html builders
+          listItem.append($('<a/>').attr('href',
+            item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
+            highlightstring + item[2]).html(item[1]));
+        }
+        if (item[3]) {
+          listItem.append($('<span> (' + item[3] + ')</span>'));
+          Search.output.append(listItem);
+          listItem.slideDown(5, function() {
+            displayNextItem();
+          });
+        } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+          $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' +
+                item[0] + '.txt', function(data) {
+            if (data != '') {
+              listItem.append($.makeSearchSummary(data, searchterms, hlterms));
+              Search.output.append(listItem);
+            }
+            listItem.slideDown(5, function() {
+              displayNextItem();
+            });
+          }, "text");
+        } else {
+          // no source available, just display title
+          Search.output.append(listItem);
+          listItem.slideDown(5, function() {
+            displayNextItem();
+          });
+        }
+      }
+      // search finished, update title and status message
+      else {
+        Search.stopPulse();
+        Search.title.text(_('Search Results'));
+        if (!resultCount)
+          Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
+        else
+            Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
+        Search.status.fadeIn(500);
+      }
+    }
+    displayNextItem();
+  },
+
+  performObjectSearch : function(object, otherterms) {
+    var filenames = this._index.filenames;
+    var objects = this._index.objects;
+    var objnames = this._index.objnames;
+    var titles = this._index.titles;
+
+    var importantResults = [];
+    var objectResults = [];
+    var unimportantResults = [];
+
+    for (var prefix in objects) {
+      for (var name in objects[prefix]) {
+        var fullname = (prefix ? prefix + '.' : '') + name;
+        if (fullname.toLowerCase().indexOf(object) > -1) {
+          var match = objects[prefix][name];
+          var objname = objnames[match[1]][2];
+          var title = titles[match[0]];
+          // If more than one term searched for, we require other words to be
+          // found in the name/title/description
+          if (otherterms.length > 0) {
+            var haystack = (prefix + ' ' + name + ' ' +
+                            objname + ' ' + title).toLowerCase();
+            var allfound = true;
+            for (var i = 0; i < otherterms.length; i++) {
+              if (haystack.indexOf(otherterms[i]) == -1) {
+                allfound = false;
+                break;
+              }
+            }
+            if (!allfound) {
+              continue;
+            }
+          }
+          var descr = objname + _(', in ') + title;
+          anchor = match[3];
+          if (anchor == '')
+            anchor = fullname;
+          else if (anchor == '-')
+            anchor = objnames[match[1]][1] + '-' + fullname;
+          result = [filenames[match[0]], fullname, '#'+anchor, descr];
+          switch (match[2]) {
+          case 1: objectResults.push(result); break;
+          case 0: importantResults.push(result); break;
+          case 2: unimportantResults.push(result); break;
+          }
+        }
+      }
+    }
+
+    // sort results descending
+    objectResults.sort(function(a, b) {
+      return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+    });
+
+    importantResults.sort(function(a, b) {
+      return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+    });
+
+    unimportantResults.sort(function(a, b) {
+      return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+    });
+
+    return [importantResults, objectResults, unimportantResults]
+  }
+}
+
+$(document).ready(function() {
+  Search.init();
+});
\ No newline at end of file
--- /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<f;e++)c.call(d,
+a[e],e,a);else{var g=b.keys(a);f=g.length;for(e=0;e<f;e++)c.call(d,a[g[e]],g[e],a)}}catch(h){if(h!=m)throw h;}return a};b.map=function(a,c,d){if(a&&b.isFunction(a.map))return a.map(c,d);var e=[];b.each(a,function(f,g,h){e.push(c.call(d,f,g,h))});return e};b.reduce=function(a,c,d,e){if(a&&b.isFunction(a.reduce))return a.reduce(b.bind(d,e),c);b.each(a,function(f,g,h){c=d.call(e,c,f,g,h)});return c};b.reduceRight=function(a,c,d,e){if(a&&b.isFunction(a.reduceRight))return a.reduceRight(b.bind(d,e),c);
+var f=b.clone(b.toArray(a)).reverse();b.each(f,function(g,h){c=d.call(e,c,g,h,a)});return c};b.detect=function(a,c,d){var e;b.each(a,function(f,g,h){if(c.call(d,f,g,h)){e=f;b.breakLoop()}});return e};b.select=function(a,c,d){if(a&&b.isFunction(a.filter))return a.filter(c,d);var e=[];b.each(a,function(f,g,h){c.call(d,f,g,h)&&e.push(f)});return e};b.reject=function(a,c,d){var e=[];b.each(a,function(f,g,h){!c.call(d,f,g,h)&&e.push(f)});return e};b.all=function(a,c,d){c=c||b.identity;if(a&&b.isFunction(a.every))return a.every(c,
+d);var e=true;b.each(a,function(f,g,h){(e=e&&c.call(d,f,g,h))||b.breakLoop()});return e};b.any=function(a,c,d){c=c||b.identity;if(a&&b.isFunction(a.some))return a.some(c,d);var e=false;b.each(a,function(f,g,h){if(e=c.call(d,f,g,h))b.breakLoop()});return e};b.include=function(a,c){if(b.isArray(a))return b.indexOf(a,c)!=-1;var d=false;b.each(a,function(e){if(d=e===c)b.breakLoop()});return d};b.invoke=function(a,c){var d=b.rest(arguments,2);return b.map(a,function(e){return(c?e[c]:e).apply(e,d)})};b.pluck=
+function(a,c){return b.map(a,function(d){return d[c]})};b.max=function(a,c,d){if(!c&&b.isArray(a))return Math.max.apply(Math,a);var e={computed:-Infinity};b.each(a,function(f,g,h){g=c?c.call(d,f,g,h):f;g>=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;g<e.computed&&(e={value:f,computed:g})});return e.value};b.sortBy=function(a,c,d){return b.pluck(b.map(a,
+function(e,f,g){return{value:e,criteria:c.call(d,e,f,g)}}).sort(function(e,f){e=e.criteria;f=f.criteria;return e<f?-1:e>f?1:0}),"value")};b.sortedIndex=function(a,c,d){d=d||b.identity;for(var e=0,f=a.length;e<f;){var g=e+f>>1;d(a[g])<d(c)?(e=g+1):(f=g)}return e};b.toArray=function(a){if(!a)return[];if(a.toArray)return a.toArray();if(b.isArray(a))return a;if(b.isArguments(a))return k.call(a);return b.values(a)};b.size=function(a){return b.toArray(a).length};b.first=function(a,c,d){return c&&!d?k.call(a,
+0,c):a[0]};b.rest=function(a,c,d){return k.call(a,b.isUndefined(c)||d?1:c)};b.last=function(a){return a[a.length-1]};b.compact=function(a){return b.select(a,function(c){return!!c})};b.flatten=function(a){return b.reduce(a,[],function(c,d){if(b.isArray(d))return c.concat(b.flatten(d));c.push(d);return c})};b.without=function(a){var c=b.rest(arguments);return b.select(a,function(d){return!b.include(c,d)})};b.uniq=function(a,c){return b.reduce(a,[],function(d,e,f){if(0==f||(c===true?b.last(d)!=e:!b.include(d,
+e)))d.push(e);return d})};b.intersect=function(a){var c=b.rest(arguments);return b.select(b.uniq(a),function(d){return b.all(c,function(e){return b.indexOf(e,d)>=0})})};b.zip=function(){for(var a=b.toArray(arguments),c=b.max(b.pluck(a,"length")),d=new Array(c),e=0;e<c;e++)d[e]=b.pluck(a,String(e));return d};b.indexOf=function(a,c){if(a.indexOf)return a.indexOf(c);for(var d=0,e=a.length;d<e;d++)if(a[d]===c)return d;return-1};b.lastIndexOf=function(a,c){if(a.lastIndexOf)return a.lastIndexOf(c);for(var d=
+a.length;d--;)if(a[d]===c)return d;return-1};b.range=function(a,c,d){var e=b.toArray(arguments),f=e.length<=1;a=f?0:e[0];c=f?e[0]:e[1];d=e[2]||1;e=Math.ceil((c-a)/d);if(e<=0)return[];e=new Array(e);f=a;for(var g=0;1;f+=d){if((d>0?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,"',$1,'").split("<%").join("');").split("%>").join("p.push('")+"');}return p.join('');");return c?a(c):a};b.forEach=b.each;b.foldl=b.inject=b.reduce;b.foldr=b.reduceRight;b.filter=b.select;b.every=b.all;b.some=b.any;b.head=b.first;b.tail=b.rest;b.methods=b.functions;var l=function(a,c){return c?b(a).chain():a};b.each(b.functions(b),function(a){var c=b[a];i.prototype[a]=function(){var d=b.toArray(arguments);
+o.call(d,this._wrapped);return l(c.apply(b,d),this._chain)}});b.each(["pop","push","reverse","shift","sort","splice","unshift"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){c.apply(this._wrapped,arguments);return l(this._wrapped,this._chain)}});b.each(["concat","join","slice"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){return l(c.apply(this._wrapped,arguments),this._chain)}});i.prototype.chain=function(){this._chain=true;return this};i.prototype.value=function(){return this._wrapped}})();
Binary file test-data/test_stats/css/up-pressed.png has changed
Binary file test-data/test_stats/css/up.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/css/websupport.js	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,808 @@
+/*
+ * websupport.js
+ * ~~~~~~~~~~~~~
+ *
+ * sphinx.websupport utilties for all documentation.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+(function($) {
+  $.fn.autogrow = function() {
+    return this.each(function() {
+    var textarea = this;
+
+    $.fn.autogrow.resize(textarea);
+
+    $(textarea)
+      .focus(function() {
+        textarea.interval = setInterval(function() {
+          $.fn.autogrow.resize(textarea);
+        }, 500);
+      })
+      .blur(function() {
+        clearInterval(textarea.interval);
+      });
+    });
+  };
+
+  $.fn.autogrow.resize = function(textarea) {
+    var lineHeight = parseInt($(textarea).css('line-height'), 10);
+    var lines = textarea.value.split('\n');
+    var columns = textarea.cols;
+    var lineCount = 0;
+    $.each(lines, function() {
+      lineCount += Math.ceil(this.length / columns) || 1;
+    });
+    var height = lineHeight * (lineCount + 1);
+    $(textarea).css('height', height);
+  };
+})(jQuery);
+
+(function($) {
+  var comp, by;
+
+  function init() {
+    initEvents();
+    initComparator();
+  }
+
+  function initEvents() {
+    $('a.comment-close').live("click", function(event) {
+      event.preventDefault();
+      hide($(this).attr('id').substring(2));
+    });
+    $('a.vote').live("click", function(event) {
+      event.preventDefault();
+      handleVote($(this));
+    });
+    $('a.reply').live("click", function(event) {
+      event.preventDefault();
+      openReply($(this).attr('id').substring(2));
+    });
+    $('a.close-reply').live("click", function(event) {
+      event.preventDefault();
+      closeReply($(this).attr('id').substring(2));
+    });
+    $('a.sort-option').live("click", function(event) {
+      event.preventDefault();
+      handleReSort($(this));
+    });
+    $('a.show-proposal').live("click", function(event) {
+      event.preventDefault();
+      showProposal($(this).attr('id').substring(2));
+    });
+    $('a.hide-proposal').live("click", function(event) {
+      event.preventDefault();
+      hideProposal($(this).attr('id').substring(2));
+    });
+    $('a.show-propose-change').live("click", function(event) {
+      event.preventDefault();
+      showProposeChange($(this).attr('id').substring(2));
+    });
+    $('a.hide-propose-change').live("click", function(event) {
+      event.preventDefault();
+      hideProposeChange($(this).attr('id').substring(2));
+    });
+    $('a.accept-comment').live("click", function(event) {
+      event.preventDefault();
+      acceptComment($(this).attr('id').substring(2));
+    });
+    $('a.delete-comment').live("click", function(event) {
+      event.preventDefault();
+      deleteComment($(this).attr('id').substring(2));
+    });
+    $('a.comment-markup').live("click", function(event) {
+      event.preventDefault();
+      toggleCommentMarkupBox($(this).attr('id').substring(2));
+    });
+  }
+
+  /**
+   * Set comp, which is a comparator function used for sorting and
+   * inserting comments into the list.
+   */
+  function setComparator() {
+    // If the first three letters are "asc", sort in ascending order
+    // and remove the prefix.
+    if (by.substring(0,3) == 'asc') {
+      var i = by.substring(3);
+      comp = function(a, b) { return a[i] - b[i]; };
+    } else {
+      // Otherwise sort in descending order.
+      comp = function(a, b) { return b[by] - a[by]; };
+    }
+
+    // Reset link styles and format the selected sort option.
+    $('a.sel').attr('href', '#').removeClass('sel');
+    $('a.by' + by).removeAttr('href').addClass('sel');
+  }
+
+  /**
+   * Create a comp function. If the user has preferences stored in
+   * the sortBy cookie, use those, otherwise use the default.
+   */
+  function initComparator() {
+    by = 'rating'; // Default to sort by rating.
+    // If the sortBy cookie is set, use that instead.
+    if (document.cookie.length > 0) {
+      var start = document.cookie.indexOf('sortBy=');
+      if (start != -1) {
+        start = start + 7;
+        var end = document.cookie.indexOf(";", start);
+        if (end == -1) {
+          end = document.cookie.length;
+          by = unescape(document.cookie.substring(start, end));
+        }
+      }
+    }
+    setComparator();
+  }
+
+  /**
+   * Show a comment div.
+   */
+  function show(id) {
+    $('#ao' + id).hide();
+    $('#ah' + id).show();
+    var context = $.extend({id: id}, opts);
+    var popup = $(renderTemplate(popupTemplate, context)).hide();
+    popup.find('textarea[name="proposal"]').hide();
+    popup.find('a.by' + by).addClass('sel');
+    var form = popup.find('#cf' + id);
+    form.submit(function(event) {
+      event.preventDefault();
+      addComment(form);
+    });
+    $('#s' + id).after(popup);
+    popup.slideDown('fast', function() {
+      getComments(id);
+    });
+  }
+
+  /**
+   * Hide a comment div.
+   */
+  function hide(id) {
+    $('#ah' + id).hide();
+    $('#ao' + id).show();
+    var div = $('#sc' + id);
+    div.slideUp('fast', function() {
+      div.remove();
+    });
+  }
+
+  /**
+   * Perform an ajax request to get comments for a node
+   * and insert the comments into the comments tree.
+   */
+  function getComments(id) {
+    $.ajax({
+     type: 'GET',
+     url: opts.getCommentsURL,
+     data: {node: id},
+     success: function(data, textStatus, request) {
+       var ul = $('#cl' + id);
+       var speed = 100;
+       $('#cf' + id)
+         .find('textarea[name="proposal"]')
+         .data('source', data.source);
+
+       if (data.comments.length === 0) {
+         ul.html('<li>No comments yet.</li>');
+         ul.data('empty', true);
+       } else {
+         // If there are comments, sort them and put them in the list.
+         var comments = sortComments(data.comments);
+         speed = data.comments.length * 100;
+         appendComments(comments, ul);
+         ul.data('empty', false);
+       }
+       $('#cn' + id).slideUp(speed + 200);
+       ul.slideDown(speed);
+     },
+     error: function(request, textStatus, error) {
+       showError('Oops, there was a problem retrieving the comments.');
+     },
+     dataType: 'json'
+    });
+  }
+
+  /**
+   * Add a comment via ajax and insert the comment into the comment tree.
+   */
+  function addComment(form) {
+    var node_id = form.find('input[name="node"]').val();
+    var parent_id = form.find('input[name="parent"]').val();
+    var text = form.find('textarea[name="comment"]').val();
+    var proposal = form.find('textarea[name="proposal"]').val();
+
+    if (text == '') {
+      showError('Please enter a comment.');
+      return;
+    }
+
+    // Disable the form that is being submitted.
+    form.find('textarea,input').attr('disabled', 'disabled');
+
+    // Send the comment to the server.
+    $.ajax({
+      type: "POST",
+      url: opts.addCommentURL,
+      dataType: 'json',
+      data: {
+        node: node_id,
+        parent: parent_id,
+        text: text,
+        proposal: proposal
+      },
+      success: function(data, textStatus, error) {
+        // Reset the form.
+        if (node_id) {
+          hideProposeChange(node_id);
+        }
+        form.find('textarea')
+          .val('')
+          .add(form.find('input'))
+          .removeAttr('disabled');
+	var ul = $('#cl' + (node_id || parent_id));
+        if (ul.data('empty')) {
+          $(ul).empty();
+          ul.data('empty', false);
+        }
+        insertComment(data.comment);
+        var ao = $('#ao' + node_id);
+        ao.find('img').attr({'src': opts.commentBrightImage});
+        if (node_id) {
+          // if this was a "root" comment, remove the commenting box
+          // (the user can get it back by reopening the comment popup)
+          $('#ca' + node_id).slideUp();
+        }
+      },
+      error: function(request, textStatus, error) {
+        form.find('textarea,input').removeAttr('disabled');
+        showError('Oops, there was a problem adding the comment.');
+      }
+    });
+  }
+
+  /**
+   * Recursively append comments to the main comment list and children
+   * lists, creating the comment tree.
+   */
+  function appendComments(comments, ul) {
+    $.each(comments, function() {
+      var div = createCommentDiv(this);
+      ul.append($(document.createElement('li')).html(div));
+      appendComments(this.children, div.find('ul.comment-children'));
+      // To avoid stagnating data, don't store the comments children in data.
+      this.children = null;
+      div.data('comment', this);
+    });
+  }
+
+  /**
+   * After adding a new comment, it must be inserted in the correct
+   * location in the comment tree.
+   */
+  function insertComment(comment) {
+    var div = createCommentDiv(comment);
+
+    // To avoid stagnating data, don't store the comments children in data.
+    comment.children = null;
+    div.data('comment', comment);
+
+    var ul = $('#cl' + (comment.node || comment.parent));
+    var siblings = getChildren(ul);
+
+    var li = $(document.createElement('li'));
+    li.hide();
+
+    // Determine where in the parents children list to insert this comment.
+    for(i=0; i < siblings.length; i++) {
+      if (comp(comment, siblings[i]) <= 0) {
+        $('#cd' + siblings[i].id)
+          .parent()
+          .before(li.html(div));
+        li.slideDown('fast');
+        return;
+      }
+    }
+
+    // If we get here, this comment rates lower than all the others,
+    // or it is the only comment in the list.
+    ul.append(li.html(div));
+    li.slideDown('fast');
+  }
+
+  function acceptComment(id) {
+    $.ajax({
+      type: 'POST',
+      url: opts.acceptCommentURL,
+      data: {id: id},
+      success: function(data, textStatus, request) {
+        $('#cm' + id).fadeOut('fast');
+        $('#cd' + id).removeClass('moderate');
+      },
+      error: function(request, textStatus, error) {
+        showError('Oops, there was a problem accepting the comment.');
+      }
+    });
+  }
+
+  function deleteComment(id) {
+    $.ajax({
+      type: 'POST',
+      url: opts.deleteCommentURL,
+      data: {id: id},
+      success: function(data, textStatus, request) {
+        var div = $('#cd' + id);
+        if (data == 'delete') {
+          // Moderator mode: remove the comment and all children immediately
+          div.slideUp('fast', function() {
+            div.remove();
+          });
+          return;
+        }
+        // User mode: only mark the comment as deleted
+        div
+          .find('span.user-id:first')
+          .text('[deleted]').end()
+          .find('div.comment-text:first')
+          .text('[deleted]').end()
+          .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
+                ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
+          .remove();
+        var comment = div.data('comment');
+        comment.username = '[deleted]';
+        comment.text = '[deleted]';
+        div.data('comment', comment);
+      },
+      error: function(request, textStatus, error) {
+        showError('Oops, there was a problem deleting the comment.');
+      }
+    });
+  }
+
+  function showProposal(id) {
+    $('#sp' + id).hide();
+    $('#hp' + id).show();
+    $('#pr' + id).slideDown('fast');
+  }
+
+  function hideProposal(id) {
+    $('#hp' + id).hide();
+    $('#sp' + id).show();
+    $('#pr' + id).slideUp('fast');
+  }
+
+  function showProposeChange(id) {
+    $('#pc' + id).hide();
+    $('#hc' + id).show();
+    var textarea = $('#pt' + id);
+    textarea.val(textarea.data('source'));
+    $.fn.autogrow.resize(textarea[0]);
+    textarea.slideDown('fast');
+  }
+
+  function hideProposeChange(id) {
+    $('#hc' + id).hide();
+    $('#pc' + id).show();
+    var textarea = $('#pt' + id);
+    textarea.val('').removeAttr('disabled');
+    textarea.slideUp('fast');
+  }
+
+  function toggleCommentMarkupBox(id) {
+    $('#mb' + id).toggle();
+  }
+
+  /** Handle when the user clicks on a sort by link. */
+  function handleReSort(link) {
+    var classes = link.attr('class').split(/\s+/);
+    for (var i=0; i<classes.length; i++) {
+      if (classes[i] != 'sort-option') {
+	by = classes[i].substring(2);
+      }
+    }
+    setComparator();
+    // Save/update the sortBy cookie.
+    var expiration = new Date();
+    expiration.setDate(expiration.getDate() + 365);
+    document.cookie= 'sortBy=' + escape(by) +
+                     ';expires=' + expiration.toUTCString();
+    $('ul.comment-ul').each(function(index, ul) {
+      var comments = getChildren($(ul), true);
+      comments = sortComments(comments);
+      appendComments(comments, $(ul).empty());
+    });
+  }
+
+  /**
+   * Function to process a vote when a user clicks an arrow.
+   */
+  function handleVote(link) {
+    if (!opts.voting) {
+      showError("You'll need to login to vote.");
+      return;
+    }
+
+    var id = link.attr('id');
+    if (!id) {
+      // Didn't click on one of the voting arrows.
+      return;
+    }
+    // If it is an unvote, the new vote value is 0,
+    // Otherwise it's 1 for an upvote, or -1 for a downvote.
+    var value = 0;
+    if (id.charAt(1) != 'u') {
+      value = id.charAt(0) == 'u' ? 1 : -1;
+    }
+    // The data to be sent to the server.
+    var d = {
+      comment_id: id.substring(2),
+      value: value
+    };
+
+    // Swap the vote and unvote links.
+    link.hide();
+    $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
+      .show();
+
+    // The div the comment is displayed in.
+    var div = $('div#cd' + d.comment_id);
+    var data = div.data('comment');
+
+    // If this is not an unvote, and the other vote arrow has
+    // already been pressed, unpress it.
+    if ((d.value !== 0) && (data.vote === d.value * -1)) {
+      $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
+      $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
+    }
+
+    // Update the comments rating in the local data.
+    data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
+    data.vote = d.value;
+    div.data('comment', data);
+
+    // Change the rating text.
+    div.find('.rating:first')
+      .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
+
+    // Send the vote information to the server.
+    $.ajax({
+      type: "POST",
+      url: opts.processVoteURL,
+      data: d,
+      error: function(request, textStatus, error) {
+        showError('Oops, there was a problem casting that vote.');
+      }
+    });
+  }
+
+  /**
+   * Open a reply form used to reply to an existing comment.
+   */
+  function openReply(id) {
+    // Swap out the reply link for the hide link
+    $('#rl' + id).hide();
+    $('#cr' + id).show();
+
+    // Add the reply li to the children ul.
+    var div = $(renderTemplate(replyTemplate, {id: id})).hide();
+    $('#cl' + id)
+      .prepend(div)
+      // Setup the submit handler for the reply form.
+      .find('#rf' + id)
+      .submit(function(event) {
+        event.preventDefault();
+        addComment($('#rf' + id));
+        closeReply(id);
+      })
+      .find('input[type=button]')
+      .click(function() {
+        closeReply(id);
+      });
+    div.slideDown('fast', function() {
+      $('#rf' + id).find('textarea').focus();
+    });
+  }
+
+  /**
+   * Close the reply form opened with openReply.
+   */
+  function closeReply(id) {
+    // Remove the reply div from the DOM.
+    $('#rd' + id).slideUp('fast', function() {
+      $(this).remove();
+    });
+
+    // Swap out the hide link for the reply link
+    $('#cr' + id).hide();
+    $('#rl' + id).show();
+  }
+
+  /**
+   * Recursively sort a tree of comments using the comp comparator.
+   */
+  function sortComments(comments) {
+    comments.sort(comp);
+    $.each(comments, function() {
+      this.children = sortComments(this.children);
+    });
+    return comments;
+  }
+
+  /**
+   * Get the children comments from a ul. If recursive is true,
+   * recursively include childrens' children.
+   */
+  function getChildren(ul, recursive) {
+    var children = [];
+    ul.children().children("[id^='cd']")
+      .each(function() {
+        var comment = $(this).data('comment');
+        if (recursive)
+          comment.children = getChildren($(this).find('#cl' + comment.id), true);
+        children.push(comment);
+      });
+    return children;
+  }
+
+  /** Create a div to display a comment in. */
+  function createCommentDiv(comment) {
+    if (!comment.displayed && !opts.moderator) {
+      return $('<div class="moderate">Thank you!  Your comment will show up '
+               + 'once it is has been approved by a moderator.</div>');
+    }
+    // Prettify the comment rating.
+    comment.pretty_rating = comment.rating + ' point' +
+      (comment.rating == 1 ? '' : 's');
+    // Make a class (for displaying not yet moderated comments differently)
+    comment.css_class = comment.displayed ? '' : ' moderate';
+    // Create a div for this comment.
+    var context = $.extend({}, opts, comment);
+    var div = $(renderTemplate(commentTemplate, context));
+
+    // If the user has voted on this comment, highlight the correct arrow.
+    if (comment.vote) {
+      var direction = (comment.vote == 1) ? 'u' : 'd';
+      div.find('#' + direction + 'v' + comment.id).hide();
+      div.find('#' + direction + 'u' + comment.id).show();
+    }
+
+    if (opts.moderator || comment.text != '[deleted]') {
+      div.find('a.reply').show();
+      if (comment.proposal_diff)
+        div.find('#sp' + comment.id).show();
+      if (opts.moderator && !comment.displayed)
+        div.find('#cm' + comment.id).show();
+      if (opts.moderator || (opts.username == comment.username))
+        div.find('#dc' + comment.id).show();
+    }
+    return div;
+  }
+
+  /**
+   * A simple template renderer. Placeholders such as <%id%> are replaced
+   * by context['id'] with items being escaped. Placeholders such as <#id#>
+   * are not escaped.
+   */
+  function renderTemplate(template, context) {
+    var esc = $(document.createElement('div'));
+
+    function handle(ph, escape) {
+      var cur = context;
+      $.each(ph.split('.'), function() {
+        cur = cur[this];
+      });
+      return escape ? esc.text(cur || "").html() : cur;
+    }
+
+    return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
+      return handle(arguments[2], arguments[1] == '%' ? true : false);
+    });
+  }
+
+  /** Flash an error message briefly. */
+  function showError(message) {
+    $(document.createElement('div')).attr({'class': 'popup-error'})
+      .append($(document.createElement('div'))
+               .attr({'class': 'error-message'}).text(message))
+      .appendTo('body')
+      .fadeIn("slow")
+      .delay(2000)
+      .fadeOut("slow");
+  }
+
+  /** Add a link the user uses to open the comments popup. */
+  $.fn.comment = function() {
+    return this.each(function() {
+      var id = $(this).attr('id').substring(1);
+      var count = COMMENT_METADATA[id];
+      var title = count + ' comment' + (count == 1 ? '' : 's');
+      var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
+      var addcls = count == 0 ? ' nocomment' : '';
+      $(this)
+        .append(
+          $(document.createElement('a')).attr({
+            href: '#',
+            'class': 'sphinx-comment-open' + addcls,
+            id: 'ao' + id
+          })
+            .append($(document.createElement('img')).attr({
+              src: image,
+              alt: 'comment',
+              title: title
+            }))
+            .click(function(event) {
+              event.preventDefault();
+              show($(this).attr('id').substring(2));
+            })
+        )
+        .append(
+          $(document.createElement('a')).attr({
+            href: '#',
+            'class': 'sphinx-comment-close hidden',
+            id: 'ah' + id
+          })
+            .append($(document.createElement('img')).attr({
+              src: opts.closeCommentImage,
+              alt: 'close',
+              title: 'close'
+            }))
+            .click(function(event) {
+              event.preventDefault();
+              hide($(this).attr('id').substring(2));
+            })
+        );
+    });
+  };
+
+  var opts = {
+    processVoteURL: '/_process_vote',
+    addCommentURL: '/_add_comment',
+    getCommentsURL: '/_get_comments',
+    acceptCommentURL: '/_accept_comment',
+    deleteCommentURL: '/_delete_comment',
+    commentImage: '/static/_static/comment.png',
+    closeCommentImage: '/static/_static/comment-close.png',
+    loadingImage: '/static/_static/ajax-loader.gif',
+    commentBrightImage: '/static/_static/comment-bright.png',
+    upArrow: '/static/_static/up.png',
+    downArrow: '/static/_static/down.png',
+    upArrowPressed: '/static/_static/up-pressed.png',
+    downArrowPressed: '/static/_static/down-pressed.png',
+    voting: false,
+    moderator: false
+  };
+
+  if (typeof COMMENT_OPTIONS != "undefined") {
+    opts = jQuery.extend(opts, COMMENT_OPTIONS);
+  }
+
+  var popupTemplate = '\
+    <div class="sphinx-comments" id="sc<%id%>">\
+      <p class="sort-options">\
+        Sort by:\
+        <a href="#" class="sort-option byrating">best rated</a>\
+        <a href="#" class="sort-option byascage">newest</a>\
+        <a href="#" class="sort-option byage">oldest</a>\
+      </p>\
+      <div class="comment-header">Comments</div>\
+      <div class="comment-loading" id="cn<%id%>">\
+        loading comments... <img src="<%loadingImage%>" alt="" /></div>\
+      <ul id="cl<%id%>" class="comment-ul"></ul>\
+      <div id="ca<%id%>">\
+      <p class="add-a-comment">Add a comment\
+        (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
+      <div class="comment-markup-box" id="mb<%id%>">\
+        reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
+        <tt>``code``</tt>, \
+        code blocks: <tt>::</tt> and an indented block after blank line</div>\
+      <form method="post" id="cf<%id%>" class="comment-form" action="">\
+        <textarea name="comment" cols="80"></textarea>\
+        <p class="propose-button">\
+          <a href="#" id="pc<%id%>" class="show-propose-change">\
+            Propose a change &#9657;\
+          </a>\
+          <a href="#" id="hc<%id%>" class="hide-propose-change">\
+            Propose a change &#9663;\
+          </a>\
+        </p>\
+        <textarea name="proposal" id="pt<%id%>" cols="80"\
+                  spellcheck="false"></textarea>\
+        <input type="submit" value="Add comment" />\
+        <input type="hidden" name="node" value="<%id%>" />\
+        <input type="hidden" name="parent" value="" />\
+      </form>\
+      </div>\
+    </div>';
+
+  var commentTemplate = '\
+    <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
+      <div class="vote">\
+        <div class="arrow">\
+          <a href="#" id="uv<%id%>" class="vote" title="vote up">\
+            <img src="<%upArrow%>" />\
+          </a>\
+          <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
+            <img src="<%upArrowPressed%>" />\
+          </a>\
+        </div>\
+        <div class="arrow">\
+          <a href="#" id="dv<%id%>" class="vote" title="vote down">\
+            <img src="<%downArrow%>" id="da<%id%>" />\
+          </a>\
+          <a href="#" id="du<%id%>" class="un vote" title="vote down">\
+            <img src="<%downArrowPressed%>" />\
+          </a>\
+        </div>\
+      </div>\
+      <div class="comment-content">\
+        <p class="tagline comment">\
+          <span class="user-id"><%username%></span>\
+          <span class="rating"><%pretty_rating%></span>\
+          <span class="delta"><%time.delta%></span>\
+        </p>\
+        <div class="comment-text comment"><#text#></div>\
+        <p class="comment-opts comment">\
+          <a href="#" class="reply hidden" id="rl<%id%>">reply &#9657;</a>\
+          <a href="#" class="close-reply" id="cr<%id%>">reply &#9663;</a>\
+          <a href="#" id="sp<%id%>" class="show-proposal">proposal &#9657;</a>\
+          <a href="#" id="hp<%id%>" class="hide-proposal">proposal &#9663;</a>\
+          <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
+          <span id="cm<%id%>" class="moderation hidden">\
+            <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
+          </span>\
+        </p>\
+        <pre class="proposal" id="pr<%id%>">\
+<#proposal_diff#>\
+        </pre>\
+          <ul class="comment-children" id="cl<%id%>"></ul>\
+        </div>\
+        <div class="clearleft"></div>\
+      </div>\
+    </div>';
+
+  var replyTemplate = '\
+    <li>\
+      <div class="reply-div" id="rd<%id%>">\
+        <form id="rf<%id%>">\
+          <textarea name="comment" cols="80"></textarea>\
+          <input type="submit" value="Add reply" />\
+          <input type="button" value="Cancel" />\
+          <input type="hidden" name="parent" value="<%id%>" />\
+          <input type="hidden" name="node" value="" />\
+        </form>\
+      </div>\
+    </li>';
+
+  $(document).ready(function() {
+    init();
+  });
+})(jQuery);
+
+$(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);
+  }
+});
--- /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
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+	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
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+	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
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+	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
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+	GL000215.1	172545	960	0.005563765974093715	0.0995128835326423
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+	GL000225.1	211173	10094	0.04779967135950145	0.2717200747790388
+	GL000192.1	547496	3452	0.006305068895480515	0.08493163306317596
+	NC_007605	171823	12864	0.07486774180406582	0.29800908736364445
+
+
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/qualimapReport.html	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,1046 @@
+<!DOCTYPE HTML>
+<html>
+	<head>
+		<link rel="stylesheet" href="css/agogo.css" type="text/css" />
+		<link rel="stylesheet" href="css/report.css" type="text/css" />
+	<title>Qualimap report: BAM QC</title>
+
+	</head>
+<body>
+	<div class="header-wrapper">
+		<div class="header">
+		<p class="logo"><a href="http://qualimap.bioinfo.cipf.es/">
+		<img class="logo" src="css/qualimap_logo_small.png" alt="Logo"/>
+		</a></p>
+<div class="headertitle"><a href="">Qualimap Report: BAM QC</a></div>
+	</div>
+</div>
+
+<div class="content-wrapper">
+<div class="content">
+<div class="document">
+<div class="documentwrapper">
+<div class="bodywrapper">
+<div class="body">
+<div class=section>
+<h2>Input data and parameters<a class="headerlink" name="input" title="Permalink to this headline">&nbsp;</a></h2>
+<div class=summary>
+
+
+<div class=table-summary>
+<h3>QualiMap command line</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>qualimap bamqc -bam ../qualimap2/test-data/test.bam -nw 400 -hm 3</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Alignment</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Command line: </td>
+<td class=column2>bwa mem -K 100000000 -p -v 3 -t 16 -Y /cromwell_root/broad-references/hg19/v0/Homo_sapiens_assembly19.fasta</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Draw chromosome limits: </td>
+<td class=column2>no
+</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Analyze overlapping paired-end reads:</td>
+<td class=column2>no
+</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Program: </td>
+<td class=column2>bwamem (0.7.15-r1140)</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Analysis date: </td>
+<td class=column2>Thu Jul 26 16:33:35 EDT 2018</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Size of a homopolymer: </td>
+<td class=column2>3</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Skip duplicate alignments: </td>
+<td class=column2>no
+</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number of windows: </td>
+<td class=column2>400</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>BAM file: </td>
+<td class=column2>../qualimap2/test-data/test.bam</td>
+</tr>
+</table>
+</div>
+
+</div>
+</div> <!-- summary section -->
+
+<div class=section>
+<h2>Summary<a class="headerlink" name="summary" title="Permalink to this headline">&nbsp;</a></h2>
+<div class=summary>
+
+
+<div class=table-summary>
+<h3>Globals</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Reference size</td>
+<td class=column2>3,101,976,562</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number of reads</td>
+<td class=column2>61,169</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mapped reads</td>
+<td class=column2>60,246 / 98.49%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Unmapped reads</td>
+<td class=column2>923 / 1.51%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mapped paired reads</td>
+<td class=column2>60,246 / 98.49%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mapped reads, first in pair</td>
+<td class=column2>30,268 / 49.48%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mapped reads,  second in pair</td>
+<td class=column2>29,978 / 49.01%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mapped reads, both in pair</td>
+<td class=column2>59,810 / 97.78%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mapped reads, singletons</td>
+<td class=column2>436 / 0.71%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Secondary alignments</td>
+<td class=column2>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Supplementary alignments</td>
+<td class=column2>1,169 / 1.91%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Read min/max/mean length</td>
+<td class=column2>250 / 250 / 250</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Duplicated reads (flagged)</td>
+<td class=column2>48 / 0.08%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Clipped reads</td>
+<td class=column2>33,606 / 54.94%</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>ACGT Content</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of A's</td>
+<td class=column2>3,912,917 / 29.53%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of C's</td>
+<td class=column2>2,699,395 / 20.37%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of T's</td>
+<td class=column2>3,942,019 / 29.75%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of G's</td>
+<td class=column2>2,694,640 / 20.34%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of N's</td>
+<td class=column2>14,397 / 0.11%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>GC Percentage</td>
+<td class=column2>40.71%</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Coverage</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mean</td>
+<td class=column2>0.0043</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Standard Deviation</td>
+<td class=column2>0.0869</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Mapping Quality</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mean Mapping Quality</td>
+<td class=column2>49.97</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Insert size</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mean</td>
+<td class=column2>75,226.79</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Standard Deviation</td>
+<td class=column2>2,849,315.96</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>P25/Median/P75</td>
+<td class=column2>339 / 427 / 535</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Mismatches and indels</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>General error rate</td>
+<td class=column2>1.49%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mismatches</td>
+<td class=column2>190,508</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Insertions</td>
+<td class=column2>2,279</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mapped reads with at least one insertion</td>
+<td class=column2>3.3%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Deletions</td>
+<td class=column2>2,316</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mapped reads with at least one deletion</td>
+<td class=column2>3.41%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Homopolymer indels</td>
+<td class=column2>50.79%</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Chromosome stats</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td><b>Name</b></td>
+<td><b>Length</b></td>
+<td><b>Mapped bases</b></td>
+<td><b>Mean coverage</b></td>
+<td><b>Standard deviation</b></td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>1</td>
+<td>249250621</td>
+<td>1063202</td>
+<td>0.0043</td>
+<td>0.1147</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>2</td>
+<td>243199373</td>
+<td>1091086</td>
+<td>0.0045</td>
+<td>0.082</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>3</td>
+<td>198022430</td>
+<td>906302</td>
+<td>0.0046</td>
+<td>0.0765</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>4</td>
+<td>191154276</td>
+<td>899976</td>
+<td>0.0047</td>
+<td>0.088</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>5</td>
+<td>180915260</td>
+<td>759318</td>
+<td>0.0042</td>
+<td>0.0739</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>6</td>
+<td>171115067</td>
+<td>734471</td>
+<td>0.0043</td>
+<td>0.0752</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>7</td>
+<td>159138663</td>
+<td>654165</td>
+<td>0.0041</td>
+<td>0.0773</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>8</td>
+<td>146364022</td>
+<td>676934</td>
+<td>0.0046</td>
+<td>0.1184</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>9</td>
+<td>141213431</td>
+<td>525097</td>
+<td>0.0037</td>
+<td>0.0766</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>10</td>
+<td>135534747</td>
+<td>724777</td>
+<td>0.0053</td>
+<td>0.1311</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>11</td>
+<td>135006516</td>
+<td>589118</td>
+<td>0.0044</td>
+<td>0.082</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>12</td>
+<td>133851895</td>
+<td>581268</td>
+<td>0.0043</td>
+<td>0.0745</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>13</td>
+<td>115169878</td>
+<td>424915</td>
+<td>0.0037</td>
+<td>0.0689</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>14</td>
+<td>107349540</td>
+<td>385363</td>
+<td>0.0036</td>
+<td>0.068</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>15</td>
+<td>102531392</td>
+<td>361006</td>
+<td>0.0035</td>
+<td>0.0671</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>16</td>
+<td>90354753</td>
+<td>405846</td>
+<td>0.0045</td>
+<td>0.0833</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>17</td>
+<td>81195210</td>
+<td>351366</td>
+<td>0.0043</td>
+<td>0.0765</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>18</td>
+<td>78077248</td>
+<td>355035</td>
+<td>0.0045</td>
+<td>0.0817</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>19</td>
+<td>59128983</td>
+<td>263166</td>
+<td>0.0045</td>
+<td>0.0888</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>20</td>
+<td>63025520</td>
+<td>262814</td>
+<td>0.0042</td>
+<td>0.0805</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>21</td>
+<td>48129895</td>
+<td>179259</td>
+<td>0.0037</td>
+<td>0.0748</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>22</td>
+<td>51304566</td>
+<td>150578</td>
+<td>0.0029</td>
+<td>0.0612</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>X</td>
+<td>155270560</td>
+<td>669025</td>
+<td>0.0043</td>
+<td>0.0753</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>Y</td>
+<td>59373566</td>
+<td>28998</td>
+<td>0.0005</td>
+<td>0.049</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MT</td>
+<td>16569</td>
+<td>56251</td>
+<td>3.395</td>
+<td>2.0903</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000207.1</td>
+<td>4262</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000226.1</td>
+<td>15008</td>
+<td>21953</td>
+<td>1.4628</td>
+<td>1.7817</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000229.1</td>
+<td>19913</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000231.1</td>
+<td>27386</td>
+<td>1169</td>
+<td>0.0427</td>
+<td>0.2278</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000210.1</td>
+<td>27682</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000239.1</td>
+<td>33824</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000235.1</td>
+<td>34474</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000201.1</td>
+<td>36148</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000247.1</td>
+<td>36422</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000245.1</td>
+<td>36651</td>
+<td>481</td>
+<td>0.0131</td>
+<td>0.1138</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000197.1</td>
+<td>37175</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000203.1</td>
+<td>37498</td>
+<td>459</td>
+<td>0.0122</td>
+<td>0.1178</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000246.1</td>
+<td>38154</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000249.1</td>
+<td>38502</td>
+<td>483</td>
+<td>0.0125</td>
+<td>0.1113</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000196.1</td>
+<td>38914</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000248.1</td>
+<td>39786</td>
+<td>456</td>
+<td>0.0115</td>
+<td>0.1064</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000244.1</td>
+<td>39929</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000238.1</td>
+<td>39939</td>
+<td>410</td>
+<td>0.0103</td>
+<td>0.1008</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000202.1</td>
+<td>40103</td>
+<td>423</td>
+<td>0.0105</td>
+<td>0.1417</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000234.1</td>
+<td>40531</td>
+<td>733</td>
+<td>0.0181</td>
+<td>0.1675</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000232.1</td>
+<td>40652</td>
+<td>543</td>
+<td>0.0134</td>
+<td>0.1194</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000206.1</td>
+<td>41001</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000240.1</td>
+<td>41933</td>
+<td>475</td>
+<td>0.0113</td>
+<td>0.1056</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000236.1</td>
+<td>41934</td>
+<td>924</td>
+<td>0.022</td>
+<td>0.1466</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000241.1</td>
+<td>42152</td>
+<td>930</td>
+<td>0.0221</td>
+<td>0.1716</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000243.1</td>
+<td>43341</td>
+<td>110</td>
+<td>0.0025</td>
+<td>0.0503</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000242.1</td>
+<td>43523</td>
+<td>444</td>
+<td>0.0102</td>
+<td>0.1005</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000230.1</td>
+<td>43691</td>
+<td>939</td>
+<td>0.0215</td>
+<td>0.1544</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000237.1</td>
+<td>45867</td>
+<td>852</td>
+<td>0.0186</td>
+<td>0.135</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000233.1</td>
+<td>45941</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000204.1</td>
+<td>81310</td>
+<td>1345</td>
+<td>0.0165</td>
+<td>0.1549</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000198.1</td>
+<td>90085</td>
+<td>1750</td>
+<td>0.0194</td>
+<td>0.1441</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000208.1</td>
+<td>92689</td>
+<td>3998</td>
+<td>0.0431</td>
+<td>0.2697</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000191.1</td>
+<td>106433</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000227.1</td>
+<td>128374</td>
+<td>476</td>
+<td>0.0037</td>
+<td>0.0608</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000228.1</td>
+<td>129120</td>
+<td>4339</td>
+<td>0.0336</td>
+<td>0.3105</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000214.1</td>
+<td>137718</td>
+<td>2220</td>
+<td>0.0161</td>
+<td>0.1342</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000221.1</td>
+<td>155397</td>
+<td>2809</td>
+<td>0.0181</td>
+<td>0.174</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000209.1</td>
+<td>159169</td>
+<td>463</td>
+<td>0.0029</td>
+<td>0.0574</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000218.1</td>
+<td>161147</td>
+<td>1369</td>
+<td>0.0085</td>
+<td>0.1116</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000220.1</td>
+<td>161802</td>
+<td>40235</td>
+<td>0.2487</td>
+<td>0.6522</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000213.1</td>
+<td>164239</td>
+<td>490</td>
+<td>0.003</td>
+<td>0.0545</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000211.1</td>
+<td>166566</td>
+<td>384</td>
+<td>0.0023</td>
+<td>0.0679</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000199.1</td>
+<td>169874</td>
+<td>21154</td>
+<td>0.1245</td>
+<td>0.5192</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000217.1</td>
+<td>172149</td>
+<td>2403</td>
+<td>0.014</td>
+<td>0.1307</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000216.1</td>
+<td>172294</td>
+<td>13420</td>
+<td>0.0779</td>
+<td>0.4454</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000215.1</td>
+<td>172545</td>
+<td>960</td>
+<td>0.0056</td>
+<td>0.0995</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000205.1</td>
+<td>174588</td>
+<td>1778</td>
+<td>0.0102</td>
+<td>0.1251</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000219.1</td>
+<td>179198</td>
+<td>1205</td>
+<td>0.0067</td>
+<td>0.092</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000224.1</td>
+<td>179693</td>
+<td>2523</td>
+<td>0.014</td>
+<td>0.1396</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000223.1</td>
+<td>180455</td>
+<td>622</td>
+<td>0.0034</td>
+<td>0.0586</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000195.1</td>
+<td>182896</td>
+<td>2173</td>
+<td>0.0119</td>
+<td>0.1236</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000212.1</td>
+<td>186858</td>
+<td>1274</td>
+<td>0.0068</td>
+<td>0.1243</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000222.1</td>
+<td>186861</td>
+<td>437</td>
+<td>0.0023</td>
+<td>0.0482</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000200.1</td>
+<td>187035</td>
+<td>370</td>
+<td>0.002</td>
+<td>0.0629</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000193.1</td>
+<td>189789</td>
+<td>3642</td>
+<td>0.0192</td>
+<td>0.1547</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000194.1</td>
+<td>191469</td>
+<td>1260</td>
+<td>0.0066</td>
+<td>0.0909</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000225.1</td>
+<td>211173</td>
+<td>10094</td>
+<td>0.0478</td>
+<td>0.2717</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>GL000192.1</td>
+<td>547496</td>
+<td>3452</td>
+<td>0.0063</td>
+<td>0.0849</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>NC_007605</td>
+<td>171823</td>
+<td>12864</td>
+<td>0.0749</td>
+<td>0.298</td>
+</tr>
+</table>
+</div>
+
+</div>
+</div> <!-- summary section -->
+
+
+
+<div class=section>
+
+<h2>Coverage across reference<a class="headerlink" name="genome_coverage_across_reference.png" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_coverage_across_reference.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Coverage Histogram<a class="headerlink" name="genome_coverage_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_coverage_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Coverage Histogram (0-50X)<a class="headerlink" name="genome_coverage_0to50_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_coverage_0to50_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Genome Fraction Coverage<a class="headerlink" name="genome_coverage_quotes.png" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_coverage_quotes.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Duplication Rate Histogram<a class="headerlink" name="genome_uniq_read_starts_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_uniq_read_starts_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapped Reads Nucleotide Content<a class="headerlink" name="genome_reads_content_per_read_position.png" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_reads_content_per_read_position.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapped Reads GC-content Distribution<a class="headerlink" name="genome_gc_content_per_window.png" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_gc_content_per_window.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapped Reads Clipping Profile<a class="headerlink" name="genome_reads_clipping_profile.png" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_reads_clipping_profile.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Homopolymer Indels<a class="headerlink" name="genome_homopolymer_indels" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_homopolymer_indels.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapping Quality Across Reference<a class="headerlink" name="genome_mapping_quality_across_reference.png" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_mapping_quality_across_reference.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapping Quality Histogram<a class="headerlink" name="genome_mapping_quality_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_mapping_quality_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Insert Size Across Reference<a class="headerlink" name="genome_insert_size_across_reference.png" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_insert_size_across_reference.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Insert Size Histogram<a class="headerlink" name="genome_insert_size_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
+
+<div><img width=100% src="images_qualimapReport/genome_insert_size_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+</div>
+
+</div>
+
+</div>
+
+</div>
+
+
+<div class="sidebar">
+<h3>Contents</h3>
+<li class="toctree-l1"><a class="reference internal" href="#input">Input data & parameters</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#summary">Summary</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_across_reference.png">Coverage across reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_histogram.png">Coverage Histogram</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_0to50_histogram.png">Coverage Histogram (0-50X)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_quotes.png">Genome Fraction Coverage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_uniq_read_starts_histogram.png">Duplication Rate Histogram</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_reads_content_per_read_position.png">Mapped Reads Nucleotide Content</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_gc_content_per_window.png">Mapped Reads GC-content Distribution</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_reads_clipping_profile.png">Mapped Reads Clipping Profile</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_homopolymer_indels">Homopolymer Indels</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_across_reference.png">Mapping Quality Across Reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_histogram.png">Mapping Quality Histogram</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_across_reference.png">Insert Size Across Reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_histogram.png">Insert Size Histogram</a></li>
+</div> <!-- sidebar -->
+
+<div class="clearer"></div>
+</div>
+
+</div>
+
+
+<div class="footer-wrapper">
+<div class="footer">
+<div class="left">
+<div class="footer">
+2018/07/26 16:33:36
+</div>
+</div>
+<div class="right">
+<div class="footer">
+Generated by QualiMap v.2.2.2-dev
+</div
+</div>
+<div class="clearer"></div>
+</div> <!-- footer -->
+</div>
+</body>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/raw_data_qualimapReport/coverage_across_reference.txt	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,485 @@
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+3.101890651E9	0.07486774180406582
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/raw_data_qualimapReport/coverage_histogram.txt	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,101 @@
+#Coverage	Number of genomic locations
+0.0	3.090980583E9
+1.0	9071159.0
+2.0	1841034.0
+3.0	36125.0
+4.0	16010.0
+5.0	8664.0
+6.0	6016.0
+7.0	3740.0
+8.0	2032.0
+9.0	1944.0
+10.0	1180.0
+11.0	969.0
+12.0	658.0
+13.0	739.0
+14.0	694.0
+15.0	622.0
+16.0	523.0
+17.0	397.0
+18.0	369.0
+19.0	256.0
+20.0	171.0
+21.0	173.0
+22.0	246.0
+23.0	250.0
+24.0	178.0
+25.0	133.0
+26.0	92.0
+27.0	111.0
+28.0	70.0
+29.0	82.0
+30.0	94.0
+31.0	119.0
+32.0	130.0
+33.0	97.0
+34.0	121.0
+35.0	101.0
+36.0	75.0
+37.0	29.0
+38.0	51.0
+39.0	27.0
+40.0	38.0
+41.0	32.0
+42.0	6.0
+43.0	1.0
+44.0	2.0
+45.0	4.0
+46.0	1.0
+47.0	2.0
+48.0	16.0
+49.0	9.0
+50.0	3.0
+51.0	11.0
+53.0	4.0
+54.0	4.0
+55.0	4.0
+56.0	1.0
+57.0	5.0
+58.0	5.0
+59.0	2.0
+60.0	4.0
+61.0	3.0
+62.0	12.0
+63.0	1.0
+64.0	5.0
+65.0	1.0
+66.0	6.0
+67.0	11.0
+68.0	8.0
+69.0	10.0
+70.0	7.0
+71.0	27.0
+72.0	23.0
+73.0	14.0
+74.0	18.0
+75.0	6.0
+76.0	12.0
+77.0	9.0
+78.0	12.0
+79.0	6.0
+80.0	11.0
+81.0	10.0
+82.0	2.0
+83.0	7.0
+84.0	6.0
+85.0	4.0
+86.0	2.0
+87.0	4.0
+88.0	4.0
+89.0	12.0
+90.0	6.0
+91.0	18.0
+92.0	5.0
+93.0	14.0
+94.0	11.0
+95.0	3.0
+96.0	3.0
+97.0	7.0
+98.0	13.0
+99.0	7.0
+100.0	4.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/raw_data_qualimapReport/duplication_rate_histogram.txt	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,51 @@
+#Duplication rate	Coverage
+1.0	55470.0
+2.0	2253.0
+3.0	35.0
+4.0	17.0
+5.0	4.0
+6.0	4.0
+7.0	1.0
+8.0	1.0
+9.0	0.0
+10.0	0.0
+11.0	0.0
+12.0	0.0
+13.0	0.0
+14.0	0.0
+15.0	0.0
+16.0	0.0
+17.0	0.0
+18.0	1.0
+19.0	0.0
+20.0	1.0
+21.0	0.0
+22.0	0.0
+23.0	0.0
+24.0	0.0
+25.0	0.0
+26.0	0.0
+27.0	0.0
+28.0	0.0
+29.0	0.0
+30.0	0.0
+31.0	0.0
+32.0	0.0
+33.0	0.0
+34.0	0.0
+35.0	0.0
+36.0	0.0
+37.0	0.0
+38.0	0.0
+39.0	0.0
+40.0	0.0
+41.0	0.0
+42.0	0.0
+43.0	0.0
+44.0	0.0
+45.0	0.0
+46.0	0.0
+47.0	0.0
+48.0	0.0
+49.0	0.0
+50.0	0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/raw_data_qualimapReport/genome_fraction_coverage.txt	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,52 @@
+#Coverage (X)	Coverage
+1.0	0.35448298142235046
+2.0	0.062051403726883336
+3.0	0.0027010520010435357
+4.0	0.0015364719573796037
+5.0	0.0010203494245359934
+6.0	7.410436391239728E-4
+7.0	5.471027798051864E-4
+8.0	4.265344929308412E-4
+9.0	3.610278728984895E-4
+10.0	2.9835815372791785E-4
+11.0	2.603178920992377E-4
+12.0	2.2907974503993955E-4
+13.0	2.078674635583866E-4
+14.0	1.8404394377569133E-4
+15.0	1.616711119396541E-4
+16.0	1.416193808125854E-4
+17.0	1.247591631567957E-4
+18.0	1.1196087174880631E-4
+19.0	1.0006523061178996E-4
+20.0	9.181242808153911E-5
+21.0	8.62998139012916E-5
+22.0	8.072272468950814E-5
+23.0	7.279229726009362E-5
+24.0	6.473291979602891E-5
+25.0	5.8994643040932715E-5
+26.0	5.4707054232494556E-5
+27.0	5.174120332185339E-5
+28.0	4.8162839732412976E-5
+29.0	4.5906214040769555E-5
+30.0	4.3262738230964715E-5
+31.0	4.0232412302998455E-5
+32.0	3.639614863004681E-5
+33.0	3.220527234759629E-5
+34.0	2.907823389364239E-5
+35.0	2.5177495203365652E-5
+36.0	2.1921506700550708E-5
+37.0	1.950369346559455E-5
+38.0	1.8568805685958978E-5
+39.0	1.692469268732566E-5
+40.0	1.605427992501518E-5
+41.0	1.4829254553205828E-5
+42.0	1.3797654233371759E-5
+43.0	1.3604229167185622E-5
+44.0	1.3571991658523075E-5
+45.0	1.350751664119798E-5
+46.0	1.3378566606547793E-5
+47.0	1.3346329097885246E-5
+48.0	1.3281854080560151E-5
+49.0	1.2766053927748544E-5
+50.0	1.2475916335574766E-5
+51.0	1.2379203809587125E-5
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/raw_data_qualimapReport/homopolymer_indels.txt	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,7 @@
+#Type of indel	Number of indels
+polyA	802
+polyC	318
+polyG	303
+polyT	911
+polyN	0
+Non-poly	2261
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/raw_data_qualimapReport/insert_size_across_reference.txt	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,485 @@
+#Position (bp)	insert size
+3877471.5	411.0869565217391
+1.16324135E7	444.9
+1.93873555E7	389.5853658536585
+2.71422975E7	449.0735294117647
+3.48972395E7	405.5128205128205
+4.26521815E7	428.4788732394366
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+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
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+3.528498615E8	452.0
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+6.165178895E8	474.04
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+6.630475415E8	450.0
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+6.903311315E8	453.0
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+7.250870775E8	423.9
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+9.732452215E8	435.5
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+1.0624845075E9	317.0
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+1.0818144095E9	430.0
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+1.1050792355E9	453.125
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+1.1981385395E9	435.1904761904762
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/raw_data_qualimapReport/insert_size_histogram.txt	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,968 @@
+#Insert size (bp)	insert size
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/raw_data_qualimapReport/mapped_reads_clipping_profile.txt	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,251 @@
+#Read position (bp)	Clipping profile
+0.0	0.9960120426149072
+1.0	0.994615894531623
+2.0	0.9869650030352259
+3.0	0.980263492235462
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+9.0	0.926037100680706
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+12.0	0.8937023110718453
+13.0	0.8816395916322703
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+20.0	0.8111620363880868
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+22.0	0.7320283630275416
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+223.0	0.6512751578903867
+224.0	0.6719939954463234
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+226.0	0.7101367610816461
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+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
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+238.0	0.9117963902312077
+239.0	0.921904502354185
+240.0	0.9328503033271325
+241.0	0.9421765725234706
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+243.0	0.958260198442904
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+245.0	0.9789790359988406
+246.0	0.9885286888885042
+247.0	0.9952860456115995
+248.0	1.001820018641369
+249.0	1.0029927830313279
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,101 @@
+#GC Content (%)	Sample
+1.0	0.0
+2.0	0.0
+3.0	0.0
+4.0	0.0
+5.0	0.0
+6.0	0.0
+7.0	0.0
+8.0	0.0
+9.0	0.0
+10.0	0.0
+11.0	0.0
+12.0	0.0
+13.0	0.0
+14.0	7.418947993174568E-5
+15.0	0.0
+16.0	0.0
+17.0	0.0
+18.0	7.418947993174568E-5
+19.0	0.0
+20.0	2.2256843979523704E-4
+21.0	4.451368795904741E-4
+22.0	8.902737591809482E-4
+23.0	5.935158394539654E-4
+24.0	7.418947993174568E-5
+25.0	3.7094739965872836E-4
+26.0	8.90273759180948E-4
+27.0	0.0019289264782253875
+28.0	0.0026708212775428445
+29.0	0.005935158394539654
+30.0	0.008828548111877735
+31.0	0.01595073818532532
+32.0	0.02336968617849989
+33.0	0.031530528970991914
+34.0	0.040062319163142665
+35.0	0.04963276207433786
+36.0	0.055790488908672754
+37.0	0.06536093181986793
+38.0	0.06521255286000445
+39.0	0.07255731137324727
+40.0	0.06639958453891238
+41.0	0.06231916314266636
+42.0	0.06061280510423622
+43.0	0.05133912011276801
+44.0	0.050448846353587054
+45.0	0.04258476148082202
+46.0	0.03561095036723792
+47.0	0.031233771051264927
+48.0	0.026634023295496703
+49.0	0.023295496698568147
+50.0	0.020402106981230062
+51.0	0.016395875064915796
+52.0	0.014318569626826917
+53.0	0.01149936938942058
+54.0	0.01068328511017138
+55.0	0.006825432153720603
+56.0	0.005341642555085689
+57.0	0.0036352845166555386
+58.0	0.004599747755768232
+59.0	0.0032643371169968098
+60.0	0.00222568439795237
+61.0	0.0014837895986349137
+62.0	9.644632391126938E-4
+63.0	8.160842792492024E-4
+64.0	8.902737591809482E-4
+65.0	8.160842792492024E-4
+66.0	2.967579197269827E-4
+67.0	2.967579197269827E-4
+68.0	8.160842792492026E-4
+69.0	2.967579197269827E-4
+70.0	0.0
+71.0	2.967579197269827E-4
+72.0	0.0
+73.0	0.0
+74.0	7.418947993174568E-5
+75.0	0.0
+76.0	7.418947993174568E-5
+77.0	7.418947993174568E-5
+78.0	0.0
+79.0	7.418947993174568E-5
+80.0	7.418947993174568E-5
+81.0	0.0
+82.0	7.418947993174568E-5
+83.0	0.0
+84.0	1.4837895986349135E-4
+85.0	0.0
+86.0	0.0
+87.0	0.0
+88.0	0.0
+89.0	0.0
+90.0	0.0
+91.0	0.0
+92.0	0.0
+93.0	0.0
+94.0	7.418947993174568E-5
+95.0	0.0
+96.0	1.4837895986349135E-4
+97.0	0.0
+98.0	0.0
+99.0	0.0
+100.0	7.418947993174568E-5
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,251 @@
+# Position (bp)	A	C	G	T	N
+0.0	26.98356558440027	22.246586970361463	19.975949635707718	30.78446629412181	0.009431515408738298
+1.0	30.18663399000848	22.29239325101329	20.34828918842492	27.1656141012348	0.007069469318503158
+2.0	30.371362130928052	20.32273976463956	18.911046907664485	30.394851196767902	0.0
+3.0	29.318623661958636	19.81121026866231	20.68488979457991	30.182933970440118	0.0023423043590284124
+4.0	30.66738277601345	18.669437698486828	20.598262656454324	28.988417709695497	1.0764991593498972
+5.0	30.957632037144517	19.243180499129426	21.186302959953572	28.61288450377249	0.0
+6.0	30.77314696966191	19.11693240460047	19.915303265221116	30.185360886770184	0.009256473746326337
+7.0	29.493416956812467	19.507021144135212	19.756046945975235	31.243514953077085	0.0
+8.0	29.21588454290573	19.8993427402675	20.067104839821667	30.8176678770051	0.0
+9.0	29.52775742030048	20.309637229754486	20.20199706852327	29.95831806522536	0.002290216196408941
+10.0	29.203217207045046	20.335391555970745	20.328556130237647	30.12827815625783	0.00455695048873294
+11.0	29.396551724137932	20.063520871143375	20.57168784029038	29.961433756805807	0.006805807622504538
+12.0	29.7289966774405	20.06871143457722	20.229188798227966	29.97310308975431	0.0
+13.0	29.559819159225352	20.130907127915606	20.103915967520635	30.2053577453384	0.0
+14.0	29.544589054904684	19.930109092538252	20.335565959543917	30.189735893013147	0.0
+15.0	29.364195330600605	19.900641596863306	20.33728390661201	30.39787916592408	0.0
+16.0	29.56240014202024	20.246760163323273	19.958281555121605	30.23255813953488	0.0
+17.0	29.592942268998605	20.030070533088644	20.299820903442633	30.0727441572512	0.0044221372189179025
+18.0	29.47447249019867	20.338311087617285	20.118056473283115	30.064754856614247	0.0044050922866834055
+19.0	29.245862780387167	19.724770642201836	20.846319301172027	30.17865765330758	0.004389622931390193
+20.0	29.496292732004985	20.089236893331293	21.053782725662167	29.360687649001555	0.0
+21.0	29.276132516178805	20.50315004500064	20.055286504092916	30.165430934727638	0.0
+22.0	29.282107853536427	20.49089906232763	20.206627349484492	30.02036573465145	0.0
+23.0	29.664638639186542	20.012210269257487	20.191153870444833	30.12778678343614	0.004210437674996316
+24.0	29.33244130375698	20.260918651084026	20.17729087830068	30.229349166858317	0.0
+25.0	29.59334066800905	20.123305586116704	20.17520187656986	30.108151869304383	0.0
+26.0	29.376158122297714	20.084414247477866	20.580605311920937	29.954704550133826	0.0041177681696520484
+27.0	29.782577570514	20.3370763535211	20.25321633838539	29.627129737579516	0.0
+28.0	29.539730256743578	20.27949301267468	20.44605134871628	29.734725381865452	0.0
+29.0	29.607256858862986	19.97050385874177	20.78871873611055	29.633520546284696	0.0
+30.0	29.47522803069876	20.514726564069594	20.52276288825491	29.47924619279142	0.008036324185317635
+31.0	29.806425863101175	20.393135102773897	20.325284374376373	29.473159050089805	0.001995609658750748
+32.0	29.467850545259523	20.346423534552965	20.56293824364857	29.61881492958306	0.003972746955882646
+33.0	29.749011857707508	19.964426877470355	20.480237154150196	29.806324110671937	0.0
+34.0	29.37798666692887	20.12939765196358	20.680025958191578	29.80669013392067	0.005899588995299994
+35.0	29.746847853795323	19.926662352687412	20.648273427848697	29.672333666686274	0.005882698982293076
+36.0	28.248664932219636	19.140861876723854	19.40689736116273	28.81594647992019	4.387629349973592
+37.0	29.849236455597705	20.1517362124307	20.38906721136076	29.608014784554033	0.001945336056803813
+38.0	29.509940434748977	20.432041463603312	20.42237177999536	29.629844511487587	0.005801810164771409
+39.0	29.449364651520987	20.467847516365037	20.36003080477474	29.71698113207547	0.005775895263765884
+40.0	29.385838842579286	20.233783654306794	20.689853406151194	29.68477531857814	0.005748778384593274
+41.0	29.72163394577681	20.254517009138954	20.46438860588022	29.54801289756358	0.011447541640432718
+42.0	29.69418204626233	20.107197840837816	20.403702506984967	29.791116264041207	0.003801341873681409
+43.0	29.379002008108213	20.208009699541545	20.64752017580419	29.759784791421968	0.005683325124085932
+44.0	29.861596268952628	20.122354185155114	20.466003285436454	29.546269896716453	0.0037763637393553747
+45.0	29.377117049303724	20.257809559653744	20.485509973654498	29.872036130974784	0.0075272864132480246
+46.0	29.747262636868154	20.046497675116246	20.34460776961152	29.86163191840408	0.0
+47.0	29.102190326680123	20.33153920909023	20.88472751738058	29.68154294684907	0.0
+48.0	29.551342988685715	20.492460250890044	20.22964081343548	29.72469197934724	0.0018639676415217433
+49.0	29.46621069065497	20.14162515798082	20.816296186157164	29.57586796520705	0.0
+50.0	29.28184984806937	20.421700140813755	20.653301711998814	29.64314829911806	0.0
+51.0	29.612583638312817	20.522346678496174	20.06949835495915	29.79557132823186	0.0
+52.0	29.384428134105413	20.2043300261867	20.27809537860067	30.131302327296865	0.001844133810349279
+53.0	29.280497452030097	20.293614437882884	20.36536232683923	30.053167025406115	0.0073587578416763255
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/raw_data_qualimapReport/mapping_quality_across_reference.txt	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,485 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stats/raw_data_qualimapReport/mapping_quality_histogram.txt	Thu Jul 26 16:40:19 2018 -0400
@@ -0,0 +1,62 @@
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