README.md

BigWig Data Fetcher for HiGlass

Quickly load data from a bigwig file in HiGlass.

Usage

The live scripts can be found at:

• https://unpkg.com/higlass-bigwig-datafetcher/dist/higlass-bigwig-datafetcher.min.js

First, register the data fetcher:

import register from "higlass-register";
import { BigwigDataFetcher } from "higlass-bigwig-datafetcher";

register(
  { dataFetcher: BigwigDataFetcher, config: BigwigDataFetcher.config },
  { pluginType: "dataFetcher" }
);

Configure the track in your view config; you should be all set from here!

[...
  {
    "type": "bar",
    "height": 80,
    "data": {
      "type": "bbi",
      "url": "https://aveit.s3.amazonaws.com/higlass/bigwig/example.chr1.10000-1160000.bw",
      "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.chrom.sizes",
    },
    "options": {
      ...
    }
    
  }
]

Note that the chromSizesUrl option is required.

For an example, see src/index.html.

Basic authentication

Bigwig files may be hosted on a website that uses Basic authentication to limit access. To load data from a bigWig file hosted on a site that uses Basic authentication, add the username and password to the URL. For example: http://username:password@example.com/data.bw. This would be used in the view configuration url property, e.g.,:

[...
  {
    "type": "bar",
    "height": 80,
    "data": {
      "type": "bbi",
      "url": "http://username:password@example.com/data.bw",
      "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.chrom.sizes",
    },
    "options": {
      ...
    }
    
  }
]

Development

Testing

To run the test suite:

npm run test

Installation

$ git clone https://github.com/higlass/higlass-bigwig-datafetcher
$ cd higlass-bigwig-datafetcher
$ npm install

If you have a local copy of higlass, you can then run this command in the higlass-bigwig-datafetcher directory:

npm link higlass

Commands

• Developmental server: npm start
• Production build: npm run build