BurrowsWheelerAligner

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.

Example (see tests)

using BurrowsWheelerAligner
const BWA = BurrowsWheelerAligner
import BWA.FASTA

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"