bionode.io

bionode-vcf

> a vcf parser in javascript


Install

You need to install the latest Node.JS first, please check 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'
`




$3

#### 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 and
samtools github page

Contributing

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