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petrelharp / ftprime_ms

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edits to simplify algorithm #65

Closed petrelharp closed 6 years ago

petrelharp commented 6 years ago

There were a couple of minor bugs; and I edited the description (hopefully) for clarity.

petrelharp commented 6 years ago

btw, I think we can delete the last ("locus") simplify implementation in sims/simplify-alg.py? Perhaps also the interval tree implementation, but I'm inclined to leave it in, because why not.

petrelharp commented 6 years ago

thanks! fixed those.

what do you think about the extra python implementations?

jeromekelleher commented 6 years ago

btw, I think we can delete the last ("locus") simplify implementation in sims/simplify-alg.py? Perhaps also the interval tree implementation, but I'm inclined to leave it in, because why not.

Sure, let's delete them both. Keeping the intervaltree version means that an external package needs to be installed which is a pain.

petrelharp commented 6 years ago

I did this, and also put the python code in at the end of the doc, so it would be in the document we upload to the biorxiv. (for submission, probably want the code as a supp file)