-
Notifications
You must be signed in to change notification settings - Fork 29
/
index.html
725 lines (662 loc) · 28.8 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
<!DOCTYPE html>
<html>
<head>
<title>Ribbon</title>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content="">
<meta name="author" content="">
<link rel="icon" type="image/png" href="images/favicon-32x32.png" sizes="32x32">
<link rel="icon" type="image/png" href="images/favicon-16x16.png" sizes="16x16">
<!-- CSS: -->
<link href='https://fonts.googleapis.com/css?family=Lato:300,900' rel='stylesheet' type='text/css'>
<!-- Bundled CSS (Bootstrap/jQuery/jQueryUI) -->
<link href="css/bundle.css" rel="stylesheet">
<!-- My d3-livesearch plugin -->
<link href="css/d3-livesearch.css" rel="stylesheet">
<link href="css/d3-superTable.css" rel="stylesheet">
<!-- My own styles -->
<link href="css/custom.css" rel="stylesheet">
</head>
<!-- NAVIGATION BAR-->
<body role="document">
<div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="."> Ribbon</a>
</div>
<div class="navbar-collapse collapse">
<ul class="nav navbar-nav" id="navbar">
<li><a id="click_getting_started_link">Getting started</a></li>
<li><a id="click_info_link">Info</a></li>
<li><a id="click_advanced_settings_link">Advanced settings</a></li>
<li class="dropdown" id="examples_navbar_item">
<a href="" class="dropdown-toggle" data-toggle="dropdown">Examples <span class="caret"></span></a>
<ul class="dropdown-menu" role="menu" id="examples_list">
<li><a href="?perma=_ribbon/ilmn_deletion_a549" target="_blank">Illumina deletion in A549 cell line (600KB)</a></li>
<li><a href="?perma=_ribbon/grch38_vs_hg19" target="_blank">hg19 against GRCh38 (2 MB)</a></li>
<li><a href="?perma=_ribbon/pacb_skbr3_tra" target="_blank">PacBio SKBR3 TRA chr16 to chr19 (5MB)</a></li>
<li><a href="?perma=_ribbon/pacb_skbr3_gene_fusion" target="_blank">PacBio SKBR3 CYTH1-EIF3H gene fusion (11MB)</a></li>
<li><a href="?perma=_ribbon/grch38_vs_gorilla" target="_blank">Gorilla against GRCh38 (12MB)</a></li>
</ul>
</li>
<li class="dropdown" id="user_data_navbar_item">
<a href="" class="dropdown-toggle" data-toggle="dropdown">My data <span class="caret"></span></a>
<ul class="dropdown-menu" role="menu" id="user_data_list">
<!-- Populated by add_user_links_to_navbar() in vis.js -->
</ul>
</li>
</ul>
</div><!--/.nav-collapse -->
</div>
</div>
<!-- End of Navigation Bar -->
<div id="left_panel">
<div id="advanced_settings_panel">
<div class="panel panel-default">
<div class="panel-heading"><h3 class="panel-title">Advanced settings</h3></div>
<div class="panel-body">
<table>
<tr><th colspan="2">Fetching from a bam file</th></tr>
<tr><td >Margin around a variant or manually entered coordinate where reads will be pulled from a bam file (use this parameter carefully as importing too much data can crash your web browser due to memory overload)</td>
<td>
<input type="number" style="width: 60%" id="bam_fetch_margin" value="100"> bp
</td>
</tr>
<tr><th colspan="2">Automation</th></tr>
<tr><td colspan="2">Make Ribbon automatically go to each variant in a bedpe file and take pictures of the multi-read view and a selection of reads. Instructions: Load a bedpe file and a bam file first, set the settings below and in the right-side panel as you want them and click Run! </td></tr>
<tr>
<td>Prefix for image files</td>
<td><input type="text" id="automation_file_prefix" value="Auto-Ribbon"></td>
</tr>
<tr>
<td>Number of reads to take pictures of (randomly selected)</td>
<td><input type="number" id="automation_max_reads_to_screenshot" value="5"></td>
</tr>
<tr>
<td>Print variant coordinates onto multi-read view</td>
<td><input type="checkbox" id="add_coordinates_to_figures"></td>
</tr>
<tr>
<td>Download a file with info and coordinates for each variant alongside the images</td>
<td><input type="checkbox" id="automation_download_info"></td>
</tr>
<tr>
<td>Only select reads with alignments that start or end near the bedpe variant</td>
<td><input type="checkbox" id="automation_pick_split_reads" checked></td>
</tr>
<tr>
<td>If a region is too large for the browser to load, automatically subsample</td>
<td><input type="checkbox" id="automation_subsample" checked></td>
</tr>
<tr>
<td style="text-indent: 50px;" >Distance:</td>
<td><input type="number" id="automation_margin_for_split" value="1000"></td>
<tr>
<td></td>
<td><button class="btn btn-secondary" id="run_automation_button" type="button">Run!</button></td>
</tr>
</table>
</div>
</div>
</div>
<div id="info_panel">
<!-- GITHUB LINK -->
<div class="panel panel-default">
<div class="panel-heading"><h3 class="panel-title">Information about Ribbon</h3></div>
<div class="panel-body">
<p>Ribbon is made by Maria Nattestad with support from Pacific Biosciences and Cold Spring Harbor Laboratory.</p>
<p>The code is open-source at <a href="https://github.com/MariaNattestad/ribbon" target="_blank">https://github.com/MariaNattestad/Ribbon</a></p>
<p>
<p><strong>Please cite our paper on the bioRxiv:</strong></p>
<p>Ribbon: Visualizing complex genome alignments and structural variation: <a href="http://biorxiv.org/content/early/2016/10/20/082123" target="_blank">http://biorxiv.org/content/early/2016/10/20/082123</a></p>
</p>
<p>Ribbon stands on the shoulders of giants:</p>
<ul>
<li>Visualizations created using <a href="https://d3js.org/">D3</a> from Mike Bostock</li>
<li>Panel and navigation bar created using styles from <a href="http://getbootstrap.com/">Bootstrap</a></li>
<li>Remote bam files are read from any publicly accessible URL using a library from <a href="http://bam.iobio.io/">Bam.iobio</a> by the Gabor Marth lab.</li>
<li>Local bam files are read using Samtools compiled into WebAssembly.</li>
</ul>
<p>Ribbon also uses two D3 plug-ins created by Maria Nattestad:</p>
<ul>
<li>Variant table with advanced filtering and sorting created using <a href="https://github.com/MariaNattestad/d3-superTable">D3-superTable</a></li>
<li>Live search for chromosome and read names created using <a href="https://github.com/MariaNattestad/d3-livesearch">D3-livesearch</a></li>
</ul>
</div>
</div>
<!-- PAPER LINK -->
<!-- <div class="panel panel-default">
<div class="panel-heading"><h3 class="panel-title">How to cite Ribbon</h3></div>
<div class="panel-body">
<p>Please cite our pre-print on the bioRxiv: <a href="" target="_blank">link text</a></p>
Citation information goes here
</div>
</div>
-->
</div>
<div id="start_panel">
<div class="panel panel-default">
<div class="panel-heading"><h3 class="panel-title">Getting started</h3></div>
<div class="panel-body">
<p>
<p><strong>Please cite our paper in Bioinformatics:</strong></p>
<p>Ribbon: intuitive visualization for complex genomic variation: <a href="https://doi.org/10.1093/bioinformatics/btaa680" target="_blank">https://doi.org/10.1093/bioinformatics/btaa680</a></p>
<p>Also see the preprint on the <a href="http://biorxiv.org/content/early/2016/10/20/082123" target="_blank">bioRxiv:</a></p>
</p>
<p>
<p><strong>Examples:</strong></p>
<p>PacBio, Illumina, and genome/assembly examples shown in the Examples tab above.</p>
</p>
<p>
<p><strong>Visualize your own alignment data:</strong></p>
<p>Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right.</p>
</p>
<p>
<p><strong>Local installation:</strong></p>
<p>You can install Ribbon locally from Github by following the instructions here: <a href="https://github.com/MariaNattestad/ribbon" target="_blank">https://github.com/MariaNattestad/Ribbon</a></p>
</p>
<p>
<p><strong>Introduction video:</strong></p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/Ih4Wf2U10-4?rel=0" frameborder="0" allowfullscreen></iframe>
</p>
</div>
</div>
</div>
<div id="svg2_panel"></div>
<div id="svg1_panel"></div>
</div>
<div id="right_panel">
<div id='user-message'></div>
<div class="panel-group" id="data_description_panel">
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" class="active" href="#collapsible_info_box">Information</a>
</h4>
</div>
<div class="panel-collapse collapse in" id="collapsible_info_box">
<div class="panel-body">
<div id="user_notes">
<label>Notes</label>
<textarea class="form-control" id="notes" placeholder="Add notes here (not saved)"></textarea>
</div>
<div>
<label>Alignment file</label>
<div id="text_alignment_file_output"></div>
</div>
<div class="hide_when_no_variants">
<label>Variant file</label>
<div id="text_variant_file_output"></div>
</div>
<div>
<label>Selected region</label>
<div id="text_region_output">(No region selected)</div>
</div>
<div class="when_bam_file_only">
<label>Bam file queried</label>
<div id="bam_fetch_info">(No bam file queried)</div>
</div>
<hr>
<div class="input-group">
<input type="text" class="form-control" id="permalink_name" placeholder="Type permalink name...">
<span class="input-group-btn">
<button class="btn btn-secondary" id="generate_permalink_button" type="button">Share permalink</button>
</span>
</div>
<hr>
<button id="screenshot_top">Download top view as png</button>
<button id="screenshot_bottom">Download bottom view as png</button>
</div>
</div>
</div>
</div>
<div class="panel-group" id="region_settings_panel">
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" class="active" href="#collapsible_region_settings_box">Multi-read settings</a>
</h4>
</div>
<div class="panel-collapse collapse in" id="collapsible_region_settings_box">
<div class="panel-body">
<ul class="nav nav-tabs">
<li class="active"><a data-toggle="tab" href="#tab_reference">Reference</a></li>
<li><a data-toggle="tab" href="#tab_reads">Reads</a></li>
<li><a data-toggle="tab" href="#tab_settings">Settings</a></li>
<li id="feature_filter_tab"><a data-toggle="tab" href="#tab_features">Filter features by type</a></li>
</ul>
<div class="tab-content">
<div id="tab_reference" class="tab-pane fade in active">
<table class="settings_table">
<col width="45%">
<col width="20%">
<col width="30%">
<tr><th colspan="3">Filter reference chromosomes</th></tr>
<tr>
<td>Zoom to chromosome</td>
<td><p id="chrom_highlighted">all</p></td>
<td>
<div id="chrom_livesearch"></div>
<button class="btn btn-secondary" type="button" id="show_all_refs">Show all</button></span>
</td>
</tr>
<tr>
<td>Minimum number of alignments:</td>
<td><p id="min_aligns_for_ref_interval_label">1</p></td>
<td> <div class="slider" id="min_aligns_for_ref_interval_slider"></div> </td>
</tr>
<tr>
<td>Maximum chromosome length:</td>
<td><input class="snug" type="number" id="max_ref_length_input"></td>
<!-- <td><span id="max_ref_length_input"></span> </td> -->
<td> <div class="slider" id="max_ref_length_slider"></div> </td>
</tr>
<tr><th colspan="3">Reference settings</th></tr>
<tr>
<td>Color scheme:</td>
<td colspan="2">
<select class="form-control" id="color_scheme_dropdown">
</select>
</td>
</tr>
<tr>
<td>Collapse reference sequences within distance:</td>
<td><input id="margin_to_merge_ref_intervals" type="number" value="10000"></td>
</tr>
<tr>
<td>Draw black border on selected region</td>
<td><input id="draw_focus_rectangle" type="checkbox" checked></td>
</tr>
</table>
</div>
<!-- Read filtering-->
<div id="tab_reads" class="tab-pane fade">
<table class="settings_table">
<col width="45%">
<col width="20%">
<col width="30%">
<tr><th colspan="3">Filter reads</th></tr>
<tr><td>Number of alignments:</td>
<td> <span id="num_aligns_range_label"></span> </td>
<td> <div class="slider" id="num_aligns_range_slider"></div> </td>
</tr>
<tr>
<td>Minimum read length:</td>
<td><input class="snug" type="number" id="min_read_length_input"></input> </td>
<td> <div class="slider" id="min_read_length_slider"></div> </td>
</tr>
<tr>
<td id="region_min_mq_title" >Minimum mapping quality: </td>
<td><span id="region_mq_label">0</span></td>
<td><div class="slider" id="region_mq_slider"></div></td>
</tr>
<tr><th colspan="3">Read settings</th></tr>
<tr>
<td>Sort reads vertically:</td>
<td colspan="2">
<select class="form-control" id="read_sorting_dropdown">
</select>
</td>
</tr>
<tr>
<td>Orient reads by:</td>
<td colspan="2">
<select class="form-control" id="read_orientation_dropdown">
</select>
</td>
</tr>
</table>
</div>
<div id="tab_features" class="tab-pane fade">
<table id="feature_type_table"></table>
</div>
<div id="tab_settings" class="tab-pane fade">
<table class="settings_table">
<col width="30%">
<col width="50%">
<col width="20%">
<tr><th colspan="3" class="hide_for_coords">Indels</th></tr>
<tr>
<td class="hide_for_coords">Show indels as:</td>
<td colspan="2">
<select class="form-control" id="show_indels_as_dropdown">
</select>
</td>
</tr>
<tr><th class="when_features_only" colspan="3">Features</th></tr>
<tr>
<td class="when_features_only">Show features as:</td>
<td colspan="2">
<select class="form-control" id="show_features_as_dropdown">
</select>
</td>
</tr>
<tr><th colspan="3" class="when_variants_only">Variants</th></tr>
<tr class="when_variants_only">
<td colspan="2">Show only the chosen variant when others are in view</td>
<td><input id="show_only_selected_variants" type="checkbox"></td>
</tr>
</table>
</div>
</div> <!-- end of tab content -->
</div>
</div>
</div>
</div>
<div class="panel-group" id="settings">
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" class="active" href="#collapsible_detail_settings_box">Single-read settings</a>
</h4>
</div>
<div class="panel-collapse collapse in" id="collapsible_detail_settings_box">
<div class="panel-body">
<div class="panel-body">
<div id="ribbon_vs_dotplot_container">
<label class="radio-inline">
<input class="ribbon_vs_dotplot" id="select_ribbon" type="radio" name="ribbon_vs_dotplot" value="ribbon">Ribbon plot
</label>
<label class="radio-inline">
<input class="ribbon_vs_dotplot" id="select_dotplot" type="radio" name="ribbon_vs_dotplot" value="dotplot">Dot plot
</label>
</div>
<ul class="nav nav-tabs">
<li class="active"><a data-toggle="tab" href="#tab_select_read">Select read</a></li>
<li><a data-toggle="tab" href="#tab_filter_alignments">Filter alignments</a></li>
<li><a data-toggle="tab" href="#tab_singleread_settings">Settings</a></li>
</ul>
<div class="tab-content">
<div id="tab_select_read" class="tab-pane fade in active">
<table class="settings_table">
<col width="50%">
<col width="20%">
<col width="30%">
<tr>
<th colspan="3">Selected read</th>
</tr>
<tr>
<td style="width:100%" colspan="3"><div id="text_read_output"></div></td>
</tr>
<tr>
<td>Search reads:</td>
<td colspan="2">
<div id="readname_livesearch"></div>
</td>
</tr>
</table>
</div>
<div id="tab_filter_alignments" class="tab-pane fade">
<table class="settings_table">
<col width="50%">
<col width="20%">
<col width="30%">
<tr>
<td id="min_mq_title">Minimum mapping quality: </td>
<td><span id="mq_label">0</span></td>
<td><div class="slider" id="mq_slider"></div></td>
</tr>
<tr>
<td>Minimum alignment length: </td>
<td><span id="align_length_label">inf</span></td>
<td><div class="slider" id="align_length_slider"></div></td>
</tr>
</table>
</div>
<div id="tab_singleread_settings" class="tab-pane fade">
<table class="settings_table">
<col width="50%">
<col width="20%">
<col width="30%">
<tr>
<td>Match reference from region view </td>
<td><input id="ref_match_region_view" type="checkbox" checked></td>
</tr>
<tr>
<td>Highlight selected read</td>
<td><input id="highlight_selected_read" type="checkbox" checked></td>
</tr>
<tr>
<td class="hide_for_coords">Minimum indel size to split: </td>
<td class="hide_for_coords"><span id="indel_size_label">inf</span></td>
<td><div class="slider" id="indel_size_slider"></div></td>
</tr>
<tr class="ribbon_settings">
<td>Alignment outlines on ribbon plot: </td>
<td><input id="outline_checkbox" type="checkbox" checked/></td>
</tr>
<!-- <tr class="dotplot_settings"><th colspan="3">Dot plot settings</th></tr> -->
<tr class="dotplot_settings">
<td>Colors on dotplot: </td>
<td><input id="colors_checkbox" type="checkbox" checked/></td>
</tr>
<!-- <tr class="ribbon_settings"><th colspan="3">Ribbon plot settings</th></tr> -->
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="panel-group">
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" class="active" href="#collapsible_alignment_input_box">Input alignments</a>
</h4>
</div>
<div class="panel-collapse collapse in" id="collapsible_alignment_input_box">
<div class="panel-body">
<ul class="nav nav-tabs">
<li class="active"><a data-toggle="tab" href="#sam">sam</a></li>
<li><a data-toggle="tab" href="#bam">load bam file</a></li>
<li><a data-toggle="tab" href="#coords">coordinates</a></li>
<li><a data-toggle="tab" href="#url_bam">bam from url</a></li>
<!-- <li><a data-toggle="tab" href="#igv">from igv</a></li> -->
</ul>
<div class="tab-content">
<!-- Sam input -->
<div id="sam" class="tab-pane fade in active">
<p>Paste a few lines from a sam file here:</p>
<textarea class="form-control" placeholder="Paste lines from a sam file" id="sam_input"></textarea>
<hr>
<p>or upload a small sam file:</p>
<input type="file" id="sam_file" />
<p>For larger files (above 10MB) see the "load bam file" tab. </p>
<span id="sam_info_icon" ><span class="glyphicon glyphicon-info-sign"></span>Instructions</span>
</div>
<!-- Bam input -->
<div id="bam" class="tab-pane fade">
<p>Select bam and corresponding index (bai/csi)</p>
<input type="file" name="files[]" id="bam_file" multiple />
<span id="bam_info_icon" ><span class="glyphicon glyphicon-info-sign"></span> Instructions</span>
</div>
<div id="url_bam" class="tab-pane fade">
<input type="text" id="bam_url_input" value="http://">
<input type="submit" id="submit_bam_url" value="Load bam file from a url">
<p>Make sure the bam file exists and that it has a corresponding index (.bai or .csi) file with an identical filename except for the addition of the .bai or .csi suffix. If the bam file does not exist or cannot be read, a header will fail to appear but there will be no error message. If the header of the bam file does not show up within about 10 seconds, loading the bam file has probably failed and you should check to make sure it actually exists at the given address. (To test for this, put the url into your web browser. If it starts downloading the bam file, then also check whether adding .bai or .csi to the url downloads the index file. If one of these does not start a download, then the file does not exist.)
</p>
<p>Note that the bam file does not get read into memory, but the index file does, so if the index file is huge, it will take a while the first time you fetch reads from the bam file.
</p>
</div>
<!-- Coords input -->
<div id="coords" class="tab-pane fade">
<p>Paste coordinates here:</p>
<textarea class="form-control" placeholder="Paste lines from a coordinates file (show-coords -lTH)" id="coords_input"></textarea>
<hr>
<p>or upload a file:</p>
<input type="file" id="coords_file" />
<span id="coords_info_icon"> <span class="glyphicon glyphicon-info-sign"></span>Instructions</span>
</div>
<!-- IGV input -->
<!-- <div id="igv" class="tab-pane fade">
<p> This feature is still being implemented and tested. When the link from IGV works, the instructions here will be as follows:
</p>
<p>
Update to the newest version of IGV. Click on a read of interest within IGV and choose "Send to Ribbon"</p>
<h4>Data from IGV:</h4>
<pre readonly id="igv_stats">(empty)</pre>
</div> -->
</div>
</div>
</div>
</div>
</div>
<div class="panel-group" id="variant_input_panel">
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" class="active" href="#collapsible_variant_upload_box">Upload variants</a>
</h4>
</div>
<div class="panel-collapse collapse in" id="collapsible_variant_upload_box">
<div class="panel-body">
<ul class="nav nav-tabs">
<li class="active"><a data-toggle="tab" href="#upload_variants">upload vcf or bed</a></li>
<li><a data-toggle="tab" href="#upload_bedpe">upload bedpe</a></li>
<li><a data-toggle="tab" href="#bed">paste bed</a></li>
<li><a data-toggle="tab" href="#vcf">paste vcf</a></li>
</ul>
<div class="tab-content">
<!-- upload variant file -->
<div id="upload_variants" class="tab-pane fade in active">
<p>Upload a .vcf or .bed file</p>
<input type="file" id="variant_file" />
<p><span class="vcf_info_icon"> <span class="glyphicon glyphicon-info-sign"></span> Instructions for .vcf file</span></p>
<p><span class="bed_info_icon"> <span class="glyphicon glyphicon-info-sign"></span> Instructions for .bed file</span></p>
</div>
<!-- upload bedpe file -->
<div id="upload_bedpe" class="tab-pane fade">
<p>Upload a .bedpe file</p>
<input type="file" id="bedpe_file" />
</div>
<!-- paste bed file -->
<div id="bed" class="tab-pane fade">
<p>Paste lines from a bed file here:</p>
<textarea class="form-control" placeholder="Paste lines from a bed file" id="bed_input"></textarea>
<span class="bed_info_icon"> <span class="glyphicon glyphicon-info-sign"></span> Instructions</span>
</div>
<!-- paste vcf file -->
<div id="vcf" class="tab-pane fade">
<p>Paste lines from a vcf file here:</p>
<textarea class="form-control" placeholder="Paste lines from a vcf file" id="vcf_input"></textarea>
<span class="vcf_info_icon"> <span class="glyphicon glyphicon-info-sign"></span> Instructions</span>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="panel-group" id="feature_input_panel">
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" class="active" href="#collapsible_feature_upload_box">Upload features</a>
</h4>
</div>
<div class="panel-collapse collapse in" id="collapsible_feature_upload_box">
<div class="panel-body">
<p>Upload a bed file with genes, repeats, or any other types of elements you want to annotate</p>
<input type="file" id="feature_bed_file" />
<p><span class="bed_info_icon"> <span class="glyphicon glyphicon-info-sign"></span> Instructions for .bed file</span></p>
</div>
</div>
</div>
</div>
<div class="panel-group" id="variant_table_panel">
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" class="active" href="#collapsible_variant_table_box">Inspect variants</a>
</h4>
</div>
<div class="panel-collapse collapse in" id="collapsible_variant_table_box">
<div class="panel-body">
<div id="variant_table_box">
<p> Showing only the first 30 variants. Sort by clicking column names. Filter by typing =chr20, >2000, etc. for each column. For bam files, click on a row in the table to fetch reads around that feature. </p>
<div id="variant_table_landing">
<!-- superTable creates a table here out of _Variants -->
</div>
</div>
</div>
</div>
</div>
</div>
<div class="panel-group" id="bedpe_table_panel">
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" class="active" href="#collapsible_bedpe_table_box">Inspect rearrangements</a>
</h4>
</div>
<div class="panel-collapse collapse in" id="collapsible_bedpe_table_box">
<div class="panel-body">
<div id="bedpe_table_box">
<p> Showing only the first 30 variants. Sort by clicking column names, and filter by typing into the text boxes for each column. For instance, type >20 or =chr2. Separate multiple filters in a single column using spaces. For bam files, click on a row in the table to fetch reads around that feature. </p>
<div id="bedpe_table_landing">
<!-- superTable creates a table here out of _Bedpe -->
</div>
</div>
</div>
</div>
</div>
</div>
<div class="panel-group" id="region_selector_panel">
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" class="active" href="#collapsible_region_picking_box">Select position</a>
</h4>
</div>
<div class="panel-collapse collapse in" id="collapsible_region_picking_box">
<div class="panel-body">
<div id="region_box">
<input class="tiny_input" type="text" id="region_chrom" placeholder="chr1"> :
<input class="small_input" type="number" id="region_start" placeholder="123456789">
<!-- - <input class="small_input" id="region_end" value="100000"> -->
<button id="region_go">Go</button>
</div>
</div>
</div>
</div>
</div>
<div class="panel-group" id="feature_table_panel">
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" class="active" href="#collapsible_feature_table_box">Inspect features</a>
</h4>
</div>
<div class="panel-collapse collapse in" id="collapsible_feature_table_box">
<div class="panel-body">
<div id="feature_table_box">
<p>Showing only the first 15 features. Sort by clicking column names. Filter by typing queries into text input boxes, e.g. =17, >200.</p>
<div id="feature_table_landing">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- Libraries (d3, jQuery, jQueryUI, bootstrap, aioli, pako, moment.js) -->
<script src="js/bundle.js"></script>
<!-- My own d3-livesearch plugin -->
<script src="js/d3-livesearch.js"></script>
<script src="js/d3-superTable.js"></script>
<script src="js/saveSvgAsPng.js"></script>
<!-- Cross-browser split -->
<script src="js/cross-browser-split.js"></script>
<!-- Main -->
<script src="js/vis.js"></script>
</body>
</html>