https://github.com/jonathanbieler/burrowswheeleraligner.jl

Binding for bwa
https://github.com/jonathanbieler/burrowswheeleraligner.jl

bioinformatics bwa julia-language

Last synced: 3 days ago
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Binding for bwa

• Host: GitHub
• URL: https://github.com/jonathanbieler/burrowswheeleraligner.jl
• Owner: jonathanBieler
• License: mit
• Created: 2022-06-03T08:32:14.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2024-09-09T13:28:36.000Z (24 days ago)
• Last Synced: 2024-09-30T15:18:21.656Z (3 days ago)
• Topics: bioinformatics, bwa, julia-language
• Language: Julia
• Homepage:
• Size: 162 KB
• Stars: 8
• Watchers: 4
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# BurrowsWheelerAligner

[![Build Status](https://github.com/jonathanBieler/BurrowsWheelerAligner.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/jonathanBieler/BurrowsWheelerAligner.jl/actions/workflows/CI.yml?query=branch%3Amain)

[![Coverage](https://codecov.io/gh/jonathanBieler/BurrowsWheelerAligner.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/jonathanBieler/BurrowsWheelerAligner.jl)

Minimal WIP bindings for bwa (https://github.com/lh3/bwa)

**Warning** : make sure you use the same version of BWA as https://github.com/JuliaBinaryWrappers/BWA_jll.jl (0.7.17) to generate the reference index.

## Usage

### Single read alignment 

```julia

using BurrowsWheelerAligner

const BWA = BurrowsWheelerAligner

import BWA.FASTA

# this folder include all the files generate by `bwa index`

index_file = joinpath(@__DIR__, "data", "genome.fa")

aligner = BWA.Aligner(index_file)

record = FASTA.Record(""">test\nGAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT""")

aln = BWA.align(aligner, record)[1]

@assert BWA.position(aln) == 1

@assert BWA.cigar(aln) == "70M"

@assert BWA.mappingquality(aln) == 60

@assert BWA.is_rev(aln) == false

@assert BWA.refname(aln, aligner) == "PhiX"

```

### Paired-end alignment 

In paired-end mode `align` will return `SAM` records (and return only the primary alignement):

```julia

    aligner = BWA.Aligner(index_file; paired = true, nthreads = 8)

    r1 = FASTA.Record("test1", "TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG")

    r2 = FASTA.Record("test1", "AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC")

    

    sam1, sam2 = BWA.align(aligner, (r1,r2))

```

Multithreading can be used by providing an array of paired records :

```julia

    using Random

    records = Tuple{FASTA.Record,FASTA.Record}[]

    for i in 1:1000

        n = randstring(rand(10:20))

        r1 = FASTA.Record(n, "TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG")

        r2 = FASTA.Record(n, "AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC")

        push!(records, (r1,r2))

    end

    alns = BWA.align(aligner, records)

```

### Additional methods

The aligner mode can be switched with :

`BWA.flag!(aligner, BWA.LibBWA.MEM_F_PE)`

`BWA.flag!(aligner, BWA.LibBWA.MEM_F_NOPAIRING)`