README.md

clj-bwa

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

Requirements

• 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.

[clj-bwa "0.1.0-SNAPSHOT"]

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

(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,

$ lein midje

Generating document

cljam uses Marginalia for generating documents.

$ lein marg -m

generates HTML documents in docs directory.

License

Copyright 2014 Xcoo, Inc.

Licensed under the Apache License, Version 2.0.