BioJulia
Export and document some more things?
First, thanks for this package! I made some functions for creating objects from my GenomicVectors.jl package using your BAM reader functions. I think I found the right functions.
Chromosome names and lengths: function GenomeInfo(name, reader::BioAlignments.BAM.Reader) GenomeInfo(name, reader.refseqnames, reader.refseqlens ) end
Chromosome name and alignment start and end positions:
read_bam = function(bam_file)
# iterate over BAM records
chr = String[]
left_pos = Int64[]
right_pos = Int64[]
for record in reader
push!(chr, BAM.refname(record))
push!(left_pos, leftposition(record))
push!(right_pos, rightposition(record))
end
DataFrame(chr = chr, left = left_pos, right = right_pos)
end
Should/could reader.refseqnames, reader.refseqlens and BAM.refname be exported? I'd be happy to add the exports, some docstrings and a bit of README text if you are open to it.
I don't know about exporing the fields like reader.* should be exprted, but this package should certainly have some sort of getter method to provide a stable api for getting that info.
