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deeptools / pyBigWig

A python extension for quick access to bigWig and bigBed files
MIT License
218 stars 49 forks source link

Add numpy support for bw.stats() #94

Closed nvictus closed 5 years ago

dpryan79 commented 5 years ago

Thanks @nvictus, do you need this in a release right away?

nvictus commented 5 years ago

Not urgent. I was just exploring using pyBigWig as a backend bigwig reader for HiGlass. Numpy output for summary statistics should improve performance, and tweaking the pure C extension code didn't turn out to be as hard as I anticipated :)

So far we have been using my kent tools cython bindings but it is proving to be a pain to install on some platforms because of compiler quirks and issues with shared libraries (openssl and libpng). I was also trying to upgrade the kent source this weekend, but it got more complex and it seems like htslib is now a hard dependency...

So now I'm also considering making a conda recipe for pybbi, but regardless, I think HiGlass could easily support both packages as "engines" for bigwigs and bigbed coverage tracks.