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