Install
Install bionode-bwa with npm:
$ npm install bionode-bwa
To use it as a command line tool, you can install it globally by adding -g
.
Usage
If you're using bionode-bwa with Node.js, you can require the module:
var bwa = // aligment path is optional, reads name used instead with sam suffix
var options = operation: 'mem' params: '-t 4'var stream = // Use BWA mem algorithm with 4 threadsvar obj = reference: 'reference.fasta.gz' reads: 'reads.fastq.gz'stream
Please read the documentation for the methods exposed by bionode-bwa.
Check BWA's documentation for the arguments that can be passed.
Command line examples
$ bionode-bwa reference.fasta.gz reads.fastq.gz --alignment out.sam$ echo '{"reference": "ref.fasta.gz", "reads": "[p1.fq, p2.fq]"}' | bionode-bwa -
Contributing
To contribute, clone this repo locally and commit your code on a separate branch.
Please write unit tests for your code, and check that everything works by running the following before opening a pull-request:
$ npm test
Please also check for code coverage:
$ npm run coverage
To rebuild the documentation using the comments in the code:
$ npm run build-docs
Check the issues for ways to contribute.
Contacts
Bruno Vieira <mail@bmpvieira.com> @bmpvieira
For BWA support contact Heng Li
License
bionode-bwa is licensed under the MIT license.
Check ChooseALicense.com for details.