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APR PR master v0p3p8 #40

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c23009a
Initial commit
alexpreynolds Nov 7, 2023
dd7c467
22 Nov 2024 patches (memory leak patches, exception handling for null…
alexpreynolds Nov 23, 2024
91b0a81
22 Nov 2024 patches (remove comments and set option default)
alexpreynolds Nov 23, 2024
bdf6457
28 Jan 2025 patches (Edited showTooltip default; removed dist from pr…
alexpreynolds Jan 29, 2025
1cda7ef
3 Feb 2025 patches (regenerate and reincorporate package-lock.json)
alexpreynolds Feb 4, 2025
ad56c48
2 Apr 2025 patches (apr-PR-master-v0p3p8 with dist)
alexpreynolds Apr 2, 2025
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5 changes: 3 additions & 2 deletions .gitignore
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Expand Up @@ -3,12 +3,13 @@
*.swo
*.swp
node_modules
dist
package-lock.json
#dist
es
*.zip
*.log
*.DS_cache
.idea/
scripts/extra
*.DS_Store
.vscode/settings.json
.vscode/settings.json
1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -92,6 +92,7 @@ The following options are available:
"faiUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa.fai",
"chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes"
},
"showTooltip": false, // If true, mouseover events over transcripts show an information tooltip
},
"width": 768,
"height": 40
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2 changes: 2 additions & 0 deletions dist/higlass-transcripts.js
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8 changes: 8 additions & 0 deletions dist/higlass-transcripts.js.LICENSE.txt
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@@ -0,0 +1,8 @@
/*!
* The buffer module from node.js, for the browser.
*
* @author Feross Aboukhadijeh <http://feross.org>
* @license MIT
*/

/*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh <https://feross.org/opensource> */
2 changes: 2 additions & 0 deletions dist/higlass-transcripts.nomin.js
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8 changes: 8 additions & 0 deletions dist/higlass-transcripts.nomin.js.LICENSE.txt
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/*!
* The buffer module from node.js, for the browser.
*
* @author Feross Aboukhadijeh <http://feross.org>
* @license MIT
*/

/*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh <https://feross.org/opensource> */
199 changes: 199 additions & 0 deletions dist/index.html
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<!doctype html> <head> <meta charset=utf-8> <meta name=viewport content="width=device-width,initial-scale=1"> <title>HiGlass Transcripts</title> <style type=text/css>.canvasjs-chart-credit{display:none}</style> <link rel=stylesheet href=https://maxcdn.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css> <link rel=stylesheet href=https://cdn.jsdelivr.net/npm/higlass@1.11.11/dist/hglib.css> <link rel=stylesheet href=hglib.css> <script src=https://cdnjs.cloudflare.com/ajax/libs/pixi.js/5.2.3/pixi.min.js></script> <script crossorigin src=https://cdn.jsdelivr.net/npm/react@16/umd/react.development.js></script> <script crossorigin src=https://cdn.jsdelivr.net/npm/react-dom@16/umd/react-dom.development.js></script> <script crossorigin src=https://cdn.jsdelivr.net/npm/higlass@1.11.11/dist/hglib.min.js></script> <script src=https://cdnjs.cloudflare.com/ajax/libs/react-bootstrap/0.32.1/react-bootstrap.min.js></script> </head> <body> Higlass transcripts track <div style=""></div> <div style=margin:auto> <div style="width:800px;border:1px solid #000" id=development-demo> </div> </div> And some other text <div style=height:1500px></div> <script type="text/javascript" src="/higlass-transcripts.js"></script></body> <script src=hglib.js></script> <script crossorigin src=https://cdn.jsdelivr.net/npm/higlass-sequence/dist/higlass-sequence.js></script> <script> var viewConfig =
{
"editable": true,
"zoomFixed": false,
"trackSourceServers": [
"http://higlass.io/api/v1"
],
"exportViewUrl": "/api/v1/viewconfs/",
"views": [
{
"tracks": {
"top": [

{
"server": "http://higlass.io/api/v1",
"tilesetUid": "NyITQvZsS_mOFNlz5C2LJg",
"uid": "Lb1oLu6rSiaIFcdrouucQg",
"type": "horizontal-chromosome-labels",
"options": {
"color": "#808080",
"stroke": "#ffffff",
"fontSize": 12,
"fontIsLeftAligned": false,
"showMousePosition": false,
"mousePositionColor": "#000000"
},
"width": 768,
"height": 30
},
{
"server": "http://higlass.io/api/v1",
"tilesetUid": "P0PLbQMwTYGy-5uPIQid7A",
"uid": "TQAcqjtiSTyrm-p1Gfcvzg",
"type": "horizontal-gene-annotations",
"options": {
"fontSize": 10,
"labelColor": "black",
"labelBackgroundColor": "#ffffff",
"labelPosition": "hidden",
"labelLeftMargin": 0,
"labelRightMargin": 0,
"labelTopMargin": 0,
"labelBottomMargin": 0,
"minHeight": 24,
"plusStrandColor": "blue",
"minusStrandColor": "red",
"trackBorderWidth": 0,
"trackBorderColor": "black",
"showMousePosition": false,
"mousePositionColor": "#000000",
"geneAnnotationHeight": 16,
"geneLabelPosition": "outside",
"geneStrandSpacing": 4,
"name": "Gene Annotations (hg38)"
},
"width": 768,
"height": 90
},
{
"uid": "fastaex",
"type": "horizontal-sequence",
"data": {
"type": "fasta",
"fastaUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa",
"faiUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa.fai",
"chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.chrom.sizes"
},
"options": {
"colorAggregationMode": "none",
"labelPosition": "topLeft",
"labelColor": "black",
"labelTextOpacity": 0.4,
"valueScaling": "linear",
"trackBorderWidth": 0,
"trackBorderColor": "white",
"name": "hg38",
"backgroundColor": "white",
"barBorder": true,
"barBorderColor": "white",
"sortLargestOnTop": true,
"extendedPreloading": false,
"colorScale": [ // A T G C N other
"#007FFF",
"#e8e500",
"#008000",
"#FF0038",
"#800080",
"#DCDCDC"
]
},
"width": 768,
"height": 25
},
{
"server": "https://cgap-higlass.com/api/v1",
"tilesetUid": "transcripts_hg38",
"uid": "transcript_annotation",
"type": "horizontal-transcripts",
"options": {
"fontSize": 9,
"labelFontColor": "#222222",
"labelBackgroundPlusStrandColor": "#ececec",
"minHeight": 24,
"plusStrandColor": "#bdbfff",
"minusStrandColor": "#fabec2",
"utrColor": "#C0EAAF",
"mousePositionColor": "#000000",
"transcriptHeight": 12,
"transcriptSpacing": 2,
"name": "Gene transcripts",
"fontFamily": "Helvetica",
"maxTexts": 100,
"showToggleTranscriptsButton": true,
//"trackHeightAdjustment": "automatic",
"startCollapsed": false,
"sequenceData": {
"type": "fasta",
"fastaUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa",
"faiUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa.fai",
"chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes"
}
},
"width": 894,
"height": 106
},

{
"server": "http://higlass.io/api/v1",
"uid": "emptytrack",
"type": "empty",
"options": {
"color": "#808080",
"stroke": "#ffffff",
"fontSize": 14,
"fontIsLeftAligned": false,
"showMousePosition": false,
"mousePositionColor": "#000000"
},
"width": 768,
"height": 100
}
],
"left": [],
"center": [],
"right": [],
"bottom": [],
"whole": [],
"gallery": []
},
"initialXDomain": [
// 2148820.8089092625,
// 2148904.489478085
// 114780590.55746861,
// 114780613.7433006
// 3020000,
// 3024000
3021674.52669861,
3021731.7217806783
// 3021672.8733434854,
// 3021717.752634499
// 451246665.4697236,
// 451268523.8166885
// 2343474001.661236,
// 2343474540.4300046
],
"initialYDomain": [
-2681156982.8645544,
-2681155573.4848976
],
"layout": {
"w": 12,
"h": 12,
"x": 0,
"y": 0
},
"uid": "AD_rIRKzRQKx3N8rbT9G4w"
}
],
"zoomLocks": {
"locksByViewUid": {},
"locksDict": {}
},
"locationLocks": {
"locksByViewUid": {},
"locksDict": {}
},
"valueScaleLocks": {
"locksByViewUid": {},
"locksDict": {}
}
}


// window.higlassApi;
const hgApi = window.hglib.viewer(
document.getElementById('development-demo'),
viewConfig,
{bounded: false}
); </script> <script>!function(e,a,t,n,g,c,o){e.GoogleAnalyticsObject=g,e.ga=e.ga||function(){(e.ga.q=e.ga.q||[]).push(arguments)},e.ga.l=1*new Date,c=a.createElement(t),o=a.getElementsByTagName(t)[0],c.async=1,c.src="https://www.google-analytics.com/analytics.js",o.parentNode.insertBefore(c,o)}(window,document,"script",0,"ga"),ga("create","UA-77756807-1","auto"),ga("send","pageview")</script>
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