jonathanbieler/burrowswheeleraligner.jl

Binding for bwa

burrowswheeleraligner.jl's Issues

Compatibility for XAM should be changed

Hi,

3 days ago XAM 0.4.x was released, finally using latest Automa 1.x so things are not breaking, but this package has compat 0.3.x XAM, do you think it could be updated ? I think API didn't change.

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could you also wrap samtools or htslib into julia lang ?

I see a gen dir in your project, and maybe you use clang.jl to automatically build some Julia library from bwa_jll. It's a good idea to build samtools or htslib because XAM.jl uses pure Julia to parse BAM files so that it lost some functions such as pileup.

I also want to do that, but I know a little about C.

Suggestions

Hi,

Thanks again for this package, this is extremely useful.

The code to get full description

description(aln::BWA.LibBWA.mem_aln_t, aligner::BWA.Aligner) = begin
        anns = unsafe_load(aligner.index.bns).anns
        anno = unsafe_load(anns, aln.rid+1).anno
        unsafe_string(anno)
end

Works just fine.

I have a small feature request, would it be possible also to access aligned query and target ?
Is that exposed somehow ? The problem I am trying to solve is count the number of differences from the reference, but score includes in matches also mismatches, I think it's only counting insertions and deletions as mismatches?

Thanks!