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APR PR master v0p4p2 #60

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APR PR master v0p4p2 #60

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bd689c4
22 Nov 2024 patches (memory leaks and null tile checks)
alexpreynolds Nov 22, 2024
3fed2c8
28 Jan 2025 patches (Remove helper scripts unnecessary for use by oth…
alexpreynolds Jan 29, 2025
f3f195d
28 Jan 2025 patches (Add dist back to .gitignore)
alexpreynolds Jan 29, 2025
662e632
Merge branch 'master' into apr-PR-master-v0p4p2
alexpreynolds Feb 4, 2025
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2 changes: 1 addition & 1 deletion .gitignore
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*.swo
*.swp
node_modules
dist
es
*.zip
*.log
*.DS_cache
.idea/
*.DS_Store
dist
2 changes: 2 additions & 0 deletions dist/higlass-sequence.js
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28 changes: 28 additions & 0 deletions dist/higlass-sequence.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> */

/**
* @license
* Copyright 2009 The Closure Library Authors
* Copyright 2020 Daniel Wirtz / The long.js Authors.
*
* 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.
*
* SPDX-License-Identifier: Apache-2.0
*/
2 changes: 2 additions & 0 deletions dist/higlass-sequence.nomin.js
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28 changes: 28 additions & 0 deletions dist/higlass-sequence.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> */

/**
* @license
* Copyright 2009 The Closure Library Authors
* Copyright 2020 Daniel Wirtz / The long.js Authors.
*
* 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.
*
* SPDX-License-Identifier: Apache-2.0
*/
1 change: 1 addition & 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 Sequence</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=hglib.css> <script src=https://cdnjs.cloudflare.com/ajax/libs/pixi.js/5.2.3/pixi.min.js></script> <script crossorigin src=https://unpkg.com/react@16/umd/react.development.js></script> <script crossorigin src=https://unpkg.com/react-dom@16/umd/react-dom.development.js></script> <script src=https://cdnjs.cloudflare.com/ajax/libs/react-bootstrap/0.32.1/react-bootstrap.min.js></script> </head> <body> Higlass sequence track <div style=""></div> <div style=margin:auto> <div style="height:1500px;width:600px;border:1px solid #000" id=development-demo> </div> </div> And some other text <div style=height:1500px></div> <script type="text/javascript" src="/higlass-sequence.js"></script></body> <script src=hglib.js></script> <script>var viewConfig={editable:!0,zoomFixed:!1,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:!1,showMousePosition:!1,mousePositionColor:"#000000"},width:20,height:30},{type:"combined",uid:"FkGY-Yv9T8avNXljXklukw",height:25,width:568,contents:[{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.mod.chrom.sizes"},options:{colorAggregationMode:"none",labelPosition:"topLeft",labelColor:"black",labelTextOpacity:.4,valueScaling:"linear",trackBorderWidth:0,trackBorderColor:"white",name:"hg38",backgroundColor:"white",barBorder:!0,barBorderColor:"white",sortLargestOnTop:!0,extendedPreloading:!1,colorScale:["#007FFF","#e8e500","#008000","#FF0038","#800080","#DCDCDC"],notificationText:"Zoom in to see nucleotides...",fontSize:16,fontFamily:"Arial",fontColor:"white",textOption:{fontSize:"32px",fontFamily:"Arial",fill:16777215,fontWeight:"bold"}},width:568,height:25},{uid:"d6KeVfkNSmq_YNj_rWJgBA",type:"viewport-projection-horizontal",fromViewUid:"JaUMrYu4TkeP9RVS5QmpYg",options:{projectionFillColor:"#777",projectionStrokeColor:"#777",projectionFillOpacity:.3,projectionStrokeOpacity:.7,strokeWidth:1}}],options:{}},{uid:"fastaex1",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.mod.chrom.sizes"},options:{colorAggregationMode:"none",labelPosition:"topLeft",labelColor:"black",labelTextOpacity:.4,valueScaling:"linear",trackBorderWidth:0,trackBorderColor:"white",name:"hg38",backgroundColor:"white",barBorder:!0,barBorderColor:"white",sortLargestOnTop:!0,extendedPreloading:!1,colorScale:["#22ca03","#c40003","#f6af08","#0000c7","#808080","#DCDCDC"],notificationText:"Zoom in to see nucleotides...",fontSize:16,fontFamily:"Arial",fontColor:"white",textOption:{fontSize:"32px",fontFamily:"Arial",fill:16777215,fontWeight:"bold"}},width:568,height:25},{uid:"fastaex2",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.mod.chrom.sizes"},options:{colorAggregationMode:"none",labelPosition:"topLeft",labelColor:"black",labelTextOpacity:.4,valueScaling:"linear",trackBorderWidth:0,trackBorderColor:"white",name:"hg38",backgroundColor:"white",barBorder:!0,barBorderColor:"white",sortLargestOnTop:!0,extendedPreloading:!1,colorScale:["#a6cee3","#1f78b4","#b2df8a","#33a02c","#808080","#DCDCDC"],notificationText:"Zoom in to see nucleotides...",fontSize:16,fontFamily:"Arial",fontColor:"white",textOption:{fontSize:"32px",fontFamily:"Arial",fill:16777215,fontWeight:"bold"}},width:568,height:25},{uid:"fastaex3",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.mod.chrom.sizes"},options:{colorAggregationMode:"none",labelPosition:"topLeft",labelColor:"black",labelTextOpacity:.4,valueScaling:"linear",trackBorderWidth:0,trackBorderColor:"white",name:"hg38",backgroundColor:"white",barBorder:!0,barBorderColor:"white",sortLargestOnTop:!0,extendedPreloading:!1,colorScale:["#2c7bb6","#abd9e9","#ffffbf","#fdae61","#808080","#DCDCDC"],notificationText:"Zoom in to see nucleotides...",fontSize:16,fontFamily:"Arial",fontColor:"white",textOption:{fontSize:"32px",fontFamily:"Arial",fill:16777215,fontWeight:"bold"}},width:568,height:25},{uid:"fastaex4",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.mod.chrom.sizes"},options:{colorAggregationMode:"none",labelPosition:"topLeft",labelColor:"black",labelTextOpacity:.4,valueScaling:"linear",trackBorderWidth:0,trackBorderColor:"white",name:"hg38",backgroundColor:"white",barBorder:!0,barBorderColor:"white",sortLargestOnTop:!0,extendedPreloading:!1,colorScale:["#08519c","#6baed6","#993404","#fe9929","#808080","#DCDCDC"],notificationText:"Zoom in to see nucleotides...",fontSize:16,fontFamily:"Arial",fontColor:"white",textOption:{fontSize:"32px",fontFamily:"Arial",fill:16777215,fontWeight:"bold"}},width:568,height:25},{server:"http://higlass.io/api/v1",uid:"emptytrack",type:"empty",options:{color:"#808080",stroke:"#ffffff",fontSize:14,fontIsLeftAligned:!1,showMousePosition:!1,mousePositionColor:"#000000"},width:568,height:200}],left:[],center:[],right:[],bottom:[],whole:[],gallery:[]},initialXDomain:[1080250.0490099243,1081419.7532662181],initialYDomain:[-2681119167.5682316,-2681119130.5001388],layout:{w:12,h:10,x:0,y:0,moved:!1,static:!1},uid:"AD_rIRKzRQKx3N8rbT9G4w"},{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:!1,showMousePosition:!1,mousePositionColor:"#000000"},width:20,height:30},{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.mod.chrom.sizes"},options:{colorAggregationMode:"none",labelPosition:"topLeft",labelColor:"black",labelTextOpacity:.4,valueScaling:"linear",trackBorderWidth:0,trackBorderColor:"white",name:"hg38",backgroundColor:"white",barBorder:!0,barBorderColor:"white",sortLargestOnTop:!0,extendedPreloading:!1,colorScale:["#007FFF","#e8e500","#008000","#FF0038","#800080","#DCDCDC"],notificationText:"Zoom in to see nucleotides...",fontSize:16,fontFamily:"Arial",fontColor:"white",textOption:{fontSize:"32px",fontFamily:"Arial",fill:16777215,fontWeight:"bold"}},width:568,height:25},{uid:"fastaex1",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.mod.chrom.sizes"},options:{colorAggregationMode:"none",labelPosition:"topLeft",labelColor:"black",labelTextOpacity:.4,valueScaling:"linear",trackBorderWidth:0,trackBorderColor:"white",name:"hg38",backgroundColor:"white",barBorder:!0,barBorderColor:"white",sortLargestOnTop:!0,extendedPreloading:!1,colorScale:["#22ca03","#c40003","#f6af08","#0000c7","#808080","#DCDCDC"],notificationText:"Zoom in to see nucleotides...",fontSize:16,fontFamily:"Arial",fontColor:"white",textOption:{fontSize:"32px",fontFamily:"Arial",fill:16777215,fontWeight:"bold"}},width:568,height:25},{uid:"fastaex2",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.mod.chrom.sizes"},options:{colorAggregationMode:"none",labelPosition:"topLeft",labelColor:"black",labelTextOpacity:.4,valueScaling:"linear",trackBorderWidth:0,trackBorderColor:"white",name:"hg38",backgroundColor:"white",barBorder:!0,barBorderColor:"white",sortLargestOnTop:!0,extendedPreloading:!1,colorScale:["#a6cee3","#1f78b4","#b2df8a","#33a02c","#808080","#DCDCDC"],notificationText:"Zoom in to see nucleotides...",fontSize:16,fontFamily:"Arial",fontColor:"white",textOption:{fontSize:"32px",fontFamily:"Arial",fill:16777215,fontWeight:"bold"}},width:568,height:25},{uid:"fastaex3",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.mod.chrom.sizes"},options:{colorAggregationMode:"none",labelPosition:"topLeft",labelColor:"black",labelTextOpacity:.4,valueScaling:"linear",trackBorderWidth:0,trackBorderColor:"white",name:"hg38",backgroundColor:"white",barBorder:!0,barBorderColor:"white",sortLargestOnTop:!0,extendedPreloading:!1,colorScale:["#08519c","#6baed6","#993404","#fe9929","#808080","#DCDCDC"],notificationText:"Zoom in to see 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4 changes: 4 additions & 0 deletions package.json
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{
"name": "Alexander Veit",
"url": "http://github.com/alexander-veit"
},
{
"name": "Alex Reynolds",
"url": "http://github.com/alexpreynolds"
}
],
"main": "./src/index.js",
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101 changes: 0 additions & 101 deletions scripts/fasta_to_hdf5.py
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