Reece Hart

*Original comment by* **Kevin Jacobs (Bitbucket: [kevinjacobs](http://bitbucket.org/kevinjacobs), GitHub: Unknown)**: ---------------------------------------- To add one more consideration: I feel strongly that the parser should not automagically infer nucleotides or amino acids not...

*Original comment by* **Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece))**: ---------------------------------------- Long discussion with Kevin Jacobs: --- On Fri, Jun 24, 2016 at 8:29 AM, Kevin Jacobs wrote: > I'm confused....

*Original comment by* **Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece))**: ---------------------------------------- Thanks Jeremy. I appreciate your effort on this!

*Original comment by* **Jeremy Muhlich (Bitbucket: [jmuhlich](http://bitbucket.org/jmuhlich), GitHub: [jmuhlich](http://github.com/jmuhlich))**: ---------------------------------------- I am writing up some notes on a wiki page here: https://bitbucket.org/jmuhlich/hgvs/wiki/Compound%20variants

*Original comment by* **Jeremy Muhlich (Bitbucket: [jmuhlich](http://bitbucket.org/jmuhlich), GitHub: [jmuhlich](http://github.com/jmuhlich))**: ---------------------------------------- Just a note that I am working on this. I've had some direct emails with Reece to discuss strategy. Currently...

The hgvs package doesn't currently support fusions and didn't exist in the HGVS recommendations at the time it was written. I'm afraid that you'll have to implement fusion support yourself,...

r. is essentially the same as n., but with an RNA alphabet. So, I think you should be able to use `g_to_n` and `n_to_g` methods, and then stitch the two...

Thanks, Kevin. There are two things going on here. pysam is getting pulled in by seqrepo, which really should be optional (#523). The second is issue you've identified regarding pysam...

Status: hgvs currently *requires* seqrepo, which in turn requires pysam. That means that it's impossible to install hgvs without installing pysam. Plan: make seqrepo *optional* in hgvs (with `extras_require`). This...

Also: Investigate whether we can pin the pickle protocol version to 2 so that the same cache works for Python 2 and 3.