https://github.com/chrovis/clj-bwa

Burrows-Wheeler Aligner (BWA) wrapper for Clojure
https://github.com/chrovis/clj-bwa

Last synced: 3 days ago
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Burrows-Wheeler Aligner (BWA) wrapper for Clojure

• Host: GitHub
• URL: https://github.com/chrovis/clj-bwa
• Owner: chrovis
• License: apache-2.0
• Created: 2014-08-04T07:01:37.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2016-02-10T07:43:39.000Z (almost 9 years ago)
• Last Synced: 2023-08-09T10:23:54.929Z (over 1 year ago)
• Language: Clojure
• Size: 174 KB
• Stars: 2
• Watchers: 9
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
clj-bwa

=======

clj-bwa is Burrows-Wheeler Aligner (BWA) wrapper for Clojure.

[![Build Status](https://travis-ci.org/chrovis/clj-bwa.svg?branch=master)](https://travis-ci.org/chrovis/clj-bwa)

Requirements

------------

- [libbwa][libbwa]

clj-bwa uses libbwa native library via Java Native Access (JNA).

Install libbwa to system or locate it on your `java.library.path`.

Usage

-----

Add the following dependency to your project.clj.

```clojure

[clj-bwa "0.1.0-SNAPSHOT"]

```

clj-bwa wraps BWA sub-commands for calling its features from Clojure codes.

```clojure

(require '[clj-bwa.core :as bwa])

;; Index database sequences in the FASTA format.

(bwa/index "path/to/reference.fa" "path/to/reference.fa" :auto false)

;; Align 70bp-1Mbp query sequences with the BWA-MEM algorithm.

(let [opt (bwa/mem-option)]

  (bwa/mem "path/to/reference.fa" "path/to/read.fq" nil "path/to/out.sam" opt)

```

## Development

### Test

To run all tests,

```bash

$ lein midje

```

### Generating document

cljam uses [Marginalia][marginalia] for generating documents.

```bash

$ lein marg -m

```

generates HTML documents in `docs` directory.

License

-------

Copyright 2014 [Xcoo, Inc.][xcoo]

Licensed under the [Apache License, Version 2.0][apache-license-2.0].

[libbwa]: https://github.com/chrovis/libbwa

[marginalia]: http://gdeer81.github.io/marginalia/

[xcoo]: http://www.xcoo.jp

[apache-license-2.0]: http://www.apache.org/licenses/LICENSE-2.0.html