https://github.com/bionode/bionode-vcf

vcf parser using javascript
https://github.com/bionode/bionode-vcf

bioinformatics bionode nodejs parser tool

Last synced: 3 months ago
JSON representation

vcf parser using javascript

• Host: GitHub
• URL: https://github.com/bionode/bionode-vcf
• Owner: bionode
• License: mit
• Created: 2015-12-04T10:25:04.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2018-03-22T17:56:13.000Z (almost 7 years ago)
• Last Synced: 2024-04-13T16:34:12.759Z (10 months ago)
• Topics: bioinformatics, bionode, nodejs, parser, tool
• Language: JavaScript
• Size: 45.9 KB
• Stars: 5
• Watchers: 19
• Forks: 7
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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# bionode-vcf

> a vcf parser in javascript

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[![npm](https://img.shields.io/npm/dt/bionode-vcf.svg?style=flat-square)](https://www.npmjs.com/package/bionode-vcf)

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## Install

You need to install the latest Node.JS first, please check [nodejs.org](http://nodejs.org) or do the following:

```bash

# Ubuntu

sudo apt-get install npm

# Mac

brew install node

# Both

npm install -g n

n stable

```

To use `bionode-vcf` as a command line tool, you can install it globally with `-g`.

```bash

npm install bionode-vcf -g

```

Or, if you want to use it as a JavaScript library, you need to install it in your local project folder inside the `node_modules` directory by doing the same command **without** `-g`.

```bash

npm i bionode-vcf # 'i' can be used as shortcut to 'install'

```

### Usage

#### vcf.read

- `vcf.read` takes params: `path`

- The supported filetypes are `vcf`, `zip` and `gz`.

```javascript

var vcf = require('bionode-vcf');

vcf.read("/path/sample.vcf");

vcf.on('data', function(feature){

    console.log(feature);

})

vcf.on('end', function(){

    console.log('end of file')

})

vcf.on('error', function(err){

    console.error('it\'s not a vcf', err)

})

```

#### vcf.readStream

- `vcf.readStream` takes params: `stream` and `extension`

- The supported extension are `vcf`, `zip` and `gz`.

```javascript

var vcf = require('bionode-vcf');

var fileStream = s3.getObject({

    Bucket: [BUCKETNAME],

    Key: [FILENAME]

}).createReadStream();  // or stream data from any other source

vcf.read(filestream, 'zip'); // default value is `vcf`

vcf.on('data', function(feature){

    console.log(feature);

})

vcf.on('end', function(){

    console.log('end of file')

})

vcf.on('error', function(err){

    console.error('it\'s not a vcf', err)

})

```

## Documentation

VCF format specifications and more information about the fileds can be found at

[1000 genomes webpage](http://www.1000genomes.org/wiki/analysis/variant%20call%20format/vcf-variant-call-format-version-41) and

[samtools github page](https://github.com/samtools/hts-specs)

## Contributing

We welcome all kinds of contributions at all levels of experience, please read the [CONTRIBUTING.md](CONTRIBUTING.md) to get started!