<commit_before><!DOCTYPE html>
<!--
  ~ Copyright 2015-2016 OpenCB
  ~
  ~ Licensed under the Apache License, Version 2.0 (the "License");
  ~ you may not use this file except in compliance with the License.
  ~ You may obtain a copy of the License at
  ~
  ~     http://www.apache.org/licenses/LICENSE-2.0
  ~
  ~ Unless required by applicable law or agreed to in writing, software
  ~ distributed under the License is distributed on an "AS IS" BASIS,
  ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  ~ See the License for the specific language governing permissions and
  ~ limitations under the License.
  -->

<html lang="en">

<head>
    <meta charset="utf-8">
    <meta name="description" content="">
    <meta name="viewport" content="width=device-width, initial-scale=1">

    <title></title>

    <!-- Favicon -->
    <!-- <link rel="icon" href="src/images/favicon.ico"> -->

    <!-- Chrome for Android theme color -->
    <meta name="theme-color" content="#000000">

    <!-- Chrome for Android Theme color -->
    <meta name="msapplication-TileColor" content="#3372DF">

    <!-- Add to homescreen for Chrome on Android -->
    <meta name="mobile-web-app-capable" content="yes">
    <meta name="application-name" content="IVA">

    <!-- Add to homescreen for Safari on iOS -->
    <meta name="apple-mobile-web-app-capable" content="yes">
    <meta name="apple-mobile-web-app-status-bar-style" content="black">
    <meta name="apple-mobile-web-app-title" content="IVA">

    <!-- Force Microsoft use latest web tech -->
    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
    <!-- END meta -->


    <!-- Load IVA configuration file, this must be located in the same folder -->
    <script src="conf/config.js"></script>
    <script src="conf/tools.js"></script>
    <script src="../lib/jsorolla/src/lib/webcomponents/PolymerUtils.js"></script>

    <!-- Load PanelApps!-->
    <script src="conf/panels.js"></script>
    <script src="conf/icd10.js"></script>

    <!-- Load IVA CSS styles -->
    <!-- build:css css/bootstrap.min.css -->
    <link rel="stylesheet" href="../node_modules/bootstrap/dist/css/bootstrap.min.css">
    <!-- /build -->

    <!-- build:css css/bootstrap-table.min.css -->
    <link rel="stylesheet" href="../node_modules/bootstrap-table/dist/bootstrap-table.min.css">
    <!-- /build -->

    <!-- build:css css/bootstrap-treeview.min.css -->
    <link rel="stylesheet" href="../node_modules/bootstrap-treeview/dist/bootstrap-treeview.min.css">
    <!-- /build -->

    <!-- build:css css/bootstrap-colorpicker.min.css -->
    <link rel="stylesheet" href="../node_modules/bootstrap-colorpicker/dist/css/bootstrap-colorpicker.min.css">
    <!-- /build -->

    <!-- build:css css/bootstrap-datetimepicker.min.css -->
    <link rel="stylesheet" href="../node_modules/eonasdan-bootstrap-datetimepicker/build/css/bootstrap-datetimepicker.min.css">
    <!-- /build -->

    <!-- build:css css/font-awesome.min.css -->
    <link rel="stylesheet" href="../node_modules/font-awesome/css/font-awesome.min.css">
    <!-- /build -->

    <!-- build:css css/jquery.qtip.min.css -->
    <link rel="stylesheet" href="../node_modules/qtip2/dist/jquery.qtip.min.css">
    <!-- /build -->

    <!-- build:css css/style.css -->
    <link rel="stylesheet" href="../lib/jsorolla/styles/css/style.css">
    <!-- /build -->

    <script>
        // Force all polyfills on
//        window.customElements = true;
//        window.customElements.forcePolyfill = true;
//        window.ShadyDOM = { force: true };
//        window.ShadyCSS = { shimcssproperties: true};
    </script>
    <!-- Load IVA Javascript dependencies -->
    <!-- build:js vendors.min.js -->
    <script type="text/javascript" src="../bower_components/webcomponentsjs/webcomponents-lite.js"></script>

    <script type="text/javascript" src="../node_modules/jquery/dist/jquery.min.js"></script>
    <script type="text/javascript" src="../node_modules/bootstrap/dist/js/bootstrap.min.js"></script>
    <script type="text/javascript" src="../node_modules/bootstrap-table/dist/bootstrap-table.min.js"></script>
    <script type="text/javascript" src="../node_modules/bootstrap-treeview/dist/bootstrap-treeview.min.js"></script>
    <script type="text/javascript" src="../node_modules/bootstrap-colorpicker/dist/js/bootstrap-colorpicker.min.js"></script>
    <script type="text/javascript" src="../node_modules/bootstrap-validator/dist/validator.min.js"></script>
    <script type="text/javascript" src="../node_modules/jspdf/dist/jspdf.debug.js"></script>
    <!--<script type="text/javascript" src="../node_modules/html2pdf/src/html2pdf.js"></script>-->

    <script type="text/javascript" src="../node_modules/moment/moment.js"></script>
    <script type="text/javascript" src="../node_modules/eonasdan-bootstrap-datetimepicker/build/js/bootstrap-datetimepicker.min.js"></script>
    <script type="text/javascript" src="../node_modules/underscore/underscore.js"></script>
    <script type="text/javascript" src="../node_modules/backbone/backbone.js"></script>
    <script type="text/javascript" src="../node_modules/highcharts/highcharts.js"></script>
    <script type="text/javascript" src="../node_modules/qtip2/dist/jquery.qtip.js"></script>
    <script type="text/javascript" src="../node_modules/urijs/src/URI.js"></script>
    <script type="text/javascript" src="../node_modules/cookies-js/dist/cookies.js"></script>
    <script type="text/javascript" src="../node_modules/crypto-js/crypto-js.js"></script>
    <!-- /build -->

    <!--JQCloud-->

    <!--<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/jqcloud/1.0.4/jqcloud.css" />-->
    <!--<script src="https://cdnjs.cloudflare.com/ajax/libs/jqcloud/1.0.4/jqcloud-1.0.4.min.js"></script>-->

    <!-- We load JSorolla dependencies -->
    <script type="text/javascript" src="../lib/jsorolla/src/lib/visualisation/lollipop.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/visualisation/pedigree.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/webcomponents/opencga/variant/variant-utils.js"></script>

    <!--<script type="text/javascript" src="../lib/jsorolla/src/lib/clients/cellbase-client-config.js"></script>-->
    <script type="text/javascript" src="../lib/jsorolla/src/lib/clients/cellbase-client.js"></script>
    <!--<script type="text/javascript" src="../lib/jsorolla/src/lib/clients/opencga-client-config.js"></script>-->
    <script type="text/javascript" src="../lib/jsorolla/src/lib/clients/opencga-client.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/clients/rest-client.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/feature-binary-search-tree.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/utils.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/svg.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/region.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/lib/cache/indexeddb-cache.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/cache/file-feature-cache.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/cache/feature-chunk-cache.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/cache/memory-store.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/cache/indexedDB-store.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/cache/bam-cache.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/lib/data-adapter/feature/feature-template-adapter.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/data-adapter/feature/feature-data-adapter.js"></script>
    <!-- ES6 -->
    <script type="text/javascript" src="../lib/jsorolla/src/lib/data-adapter/feature/cellbase-adapter-new.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/data-adapter/feature/opencga-adapter-new.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/feature/info/info-widget.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/feature/info/gene-info-widget.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/feature/info/protein-info-widget.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/feature/info/snp-info-widget.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/feature/info/transcript-info-widget.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/feature/info/vcf-variant-info-widget.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/ux-window.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/navigation-bar.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/chromosome-panel.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/karyotype-panel.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/status-bar.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/tracks/tracklist-panel.js"></script>
    <!--<script type="text/javascript" src="../lib/jsorolla/src/genome-browser/tracks/track.js"></script>-->
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/tracks/feature-track.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/tracks/gene-track.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/tracks/alignment-track.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/renderer.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/feature-renderer.js"></script>
    <!--<script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/feature-cluster-renderer.js"></script>-->
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/sequence-renderer.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/histogram-renderer.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/gene-renderer.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/alignment-renderer.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/variant-renderer.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/config.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/genome-browser.js"></script>

    <!-- Loading iva-app component -->
    <link rel="import" href="iva-app.html">

</head>

<body onload="setTitle()">
    <script>
        function setTitle() {
            $("title").text(application.title);
        }

    </script>
<commit_msg>Fix javascript links at index.html<commit_after><!DOCTYPE html>
<!--
  ~ Copyright 2015-2016 OpenCB
  ~
  ~ Licensed under the Apache License, Version 2.0 (the "License");
  ~ you may not use this file except in compliance with the License.
  ~ You may obtain a copy of the License at
  ~
  ~     http://www.apache.org/licenses/LICENSE-2.0
  ~
  ~ Unless required by applicable law or agreed to in writing, software
  ~ distributed under the License is distributed on an "AS IS" BASIS,
  ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  ~ See the License for the specific language governing permissions and
  ~ limitations under the License.
  -->

<html lang="en">

<head>
    <meta charset="utf-8">
    <meta name="description" content="">
    <meta name="viewport" content="width=device-width, initial-scale=1">

    <title></title>

    <!-- Favicon -->
    <!-- <link rel="icon" href="src/images/favicon.ico"> -->

    <!-- Chrome for Android theme color -->
    <meta name="theme-color" content="#000000">

    <!-- Chrome for Android Theme color -->
    <meta name="msapplication-TileColor" content="#3372DF">

    <!-- Add to homescreen for Chrome on Android -->
    <meta name="mobile-web-app-capable" content="yes">
    <meta name="application-name" content="IVA">

    <!-- Add to homescreen for Safari on iOS -->
    <meta name="apple-mobile-web-app-capable" content="yes">
    <meta name="apple-mobile-web-app-status-bar-style" content="black">
    <meta name="apple-mobile-web-app-title" content="IVA">

    <!-- Force Microsoft use latest web tech -->
    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
    <!-- END meta -->


    <!-- Load IVA configuration file, this must be located in the same folder -->
    <script src="conf/config.js"></script>
    <script src="conf/tools.js"></script>
    <script src="../lib/jsorolla/src/lib/webcomponents/PolymerUtils.js"></script>

    <!-- Load PanelApps!-->
    <script src="conf/panels.js"></script>
    <script src="conf/icd10.js"></script>

    <!-- Load IVA CSS styles -->
    <!-- build:css css/bootstrap.min.css -->
    <link rel="stylesheet" href="../node_modules/bootstrap/dist/css/bootstrap.min.css">
    <!-- /build -->

    <!-- build:css css/bootstrap-table.min.css -->
    <link rel="stylesheet" href="../node_modules/bootstrap-table/dist/bootstrap-table.min.css">
    <!-- /build -->

    <!-- build:css css/bootstrap-treeview.min.css -->
    <link rel="stylesheet" href="../node_modules/bootstrap-treeview/dist/bootstrap-treeview.min.css">
    <!-- /build -->

    <!-- build:css css/bootstrap-colorpicker.min.css -->
    <link rel="stylesheet" href="../node_modules/bootstrap-colorpicker/dist/css/bootstrap-colorpicker.min.css">
    <!-- /build -->

    <!-- build:css css/bootstrap-datetimepicker.min.css -->
    <link rel="stylesheet" href="../node_modules/eonasdan-bootstrap-datetimepicker/build/css/bootstrap-datetimepicker.min.css">
    <!-- /build -->

    <!-- build:css css/font-awesome.min.css -->
    <link rel="stylesheet" href="../node_modules/font-awesome/css/font-awesome.min.css">
    <!-- /build -->

    <!-- build:css css/jquery.qtip.min.css -->
    <link rel="stylesheet" href="../node_modules/qtip2/dist/jquery.qtip.min.css">
    <!-- /build -->

    <!-- build:css css/style.css -->
    <link rel="stylesheet" href="../lib/jsorolla/styles/css/style.css">
    <!-- /build -->

    <script>
        // Force all polyfills on
//        window.customElements = true;
//        window.customElements.forcePolyfill = true;
//        window.ShadyDOM = { force: true };
//        window.ShadyCSS = { shimcssproperties: true};
    </script>
    <!-- Load IVA Javascript dependencies -->
    <!-- build:js vendors.min.js -->
    <script type="text/javascript" src="../bower_components/webcomponentsjs/webcomponents-lite.js"></script>

    <script type="text/javascript" src="../node_modules/jquery/dist/jquery.min.js"></script>
    <script type="text/javascript" src="../node_modules/bootstrap/dist/js/bootstrap.min.js"></script>
    <script type="text/javascript" src="../node_modules/bootstrap-table/dist/bootstrap-table.min.js"></script>
    <script type="text/javascript" src="../node_modules/bootstrap-treeview/dist/bootstrap-treeview.min.js"></script>
    <script type="text/javascript" src="../node_modules/bootstrap-colorpicker/dist/js/bootstrap-colorpicker.min.js"></script>
    <script type="text/javascript" src="../node_modules/bootstrap-validator/dist/validator.min.js"></script>
    <script type="text/javascript" src="../node_modules/jspdf/dist/jspdf.debug.js"></script>
    <!--<script type="text/javascript" src="../node_modules/html2pdf/src/html2pdf.js"></script>-->

    <script type="text/javascript" src="../node_modules/moment/moment.js"></script>
    <script type="text/javascript" src="../node_modules/eonasdan-bootstrap-datetimepicker/build/js/bootstrap-datetimepicker.min.js"></script>
    <script type="text/javascript" src="../node_modules/underscore/underscore.js"></script>
    <script type="text/javascript" src="../node_modules/backbone/backbone.js"></script>
    <script type="text/javascript" src="../node_modules/highcharts/highcharts.js"></script>
    <script type="text/javascript" src="../node_modules/qtip2/dist/jquery.qtip.js"></script>
    <script type="text/javascript" src="../node_modules/urijs/src/URI.js"></script>
    <script type="text/javascript" src="../node_modules/cookies-js/dist/cookies.js"></script>
    <script type="text/javascript" src="../node_modules/crypto-js/crypto-js.js"></script>
    <!-- /build -->

    <!--JQCloud-->

    <!--<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/jqcloud/1.0.4/jqcloud.css" />-->
    <!--<script src="https://cdnjs.cloudflare.com/ajax/libs/jqcloud/1.0.4/jqcloud-1.0.4.min.js"></script>-->

    <!-- We load JSorolla dependencies -->
    <script type="text/javascript" src="../lib/jsorolla/src/lib/visualisation/lollipop.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/visualisation/pedigree.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/webcomponents/opencga/variant/variant-utils.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/lib/clients/cellbase-client.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/clients/opencga-client.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/clients/rest-client.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/feature-binary-search-tree.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/utils.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/svg.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/region.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/lib/cache/indexeddb-cache.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/cache/file-feature-cache.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/cache/feature-chunk-cache.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/cache/memory-store.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/cache/indexedDB-store.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/cache/bam-cache.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/lib/data-adapter/feature-template-adapter.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/data-adapter/feature-adapter.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/data-adapter/cellbase-adapter.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/data-adapter/opencga-adapter.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/feature/info/info-widget.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/feature/info/gene-info-widget.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/feature/info/protein-info-widget.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/feature/info/snp-info-widget.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/feature/info/transcript-info-widget.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/feature/info/vcf-variant-info-widget.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/lib/widgets/ux-window.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/navigation-bar.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/chromosome-panel.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/karyotype-panel.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/status-bar.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/tracks/tracklist-panel.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/tracks/feature-track.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/tracks/gene-track.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/tracks/alignment-track.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/renderer.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/feature-renderer.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/sequence-renderer.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/histogram-renderer.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/gene-renderer.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/alignment-renderer.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/renderers/variant-renderer.js"></script>

    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/config.js"></script>
    <script type="text/javascript" src="../lib/jsorolla/src/genome-browser/genome-browser.js"></script>

    <!-- Loading iva-app component -->
    <link rel="import" href="iva-app.html">

</head>

<body onload="setTitle()">
    <script>
        function setTitle() {
            $("title").text(application.title);
        }

    </script>

{'fraction_non_alphanumeric': 0.20270148174918684, 'fraction_numerical': 0.0035688471268521863, 'mean_word_length': 3.6350502512562812, 'pattern_counts': {'":': 0, '<': 428, '<?xml version=': 0, '>': 428, 'https://': 4, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3165713', 'n_tokens_mistral': 7178, 'n_tokens_neox': 6853, 'n_words': 947}