implement copy number variation (invitae grammar additions) about hgvs HOT 7 CLOSED

Original comment by Reece Hart (Bitbucket: reece, GitHub: reece):

Removing milestone: milestone 4 (automated comment)

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Original comment by Rudolph Rico (Bitbucket: rrico, GitHub: rrico):

• pushed the more significant architectural change into branch iv_grammar
• incorporated the simplest solution (checkin d49e11c) - just added directly to the base grammar & edit.py & tests; all simple changes.

This gets us parsing these; if we choose to revisit the grammar import later, it's available in the branch.

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Original comment by Rudolph Rico (Bitbucket: rrico, GitHub: rrico):

re-opening since branching this actually requires implementing the simpler solution (extend hgvs.meta & edit.py) as well.

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Original comment by Rudolph Rico (Bitbucket: rrico, GitHub: rrico):

Per conversation w/ RH, pushing this into a branch for now.

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Original comment by Rudolph Rico (Bitbucket: rrico, GitHub: rrico):

One additional note - remaining task is to enable more tests from the hgvs-test repository - should be quick.

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Original comment by Rudolph Rico (Bitbucket: rrico, GitHub: rrico):

See 2283bba

Probably worth a short code review - here's a summary.

What it does:

• supports parsing copyN, dupN for NAs.
  How it does it:
• extended the Parser class to take a few more arguments (which can all be omitted by default)
  -- parser can either take use_internal which enables the extended grammar OR take a file, variable dictionary, and modules to import. This latter three allows the user to arbitrarily extend the grammar - without requiring any edits to the hgvs.parser module.

I tried to abstract out the invitae-specific code from any existing code, so the additional edit methods and test live in their own files.

In [7]: var_c = p2.parse_hgvs_variant('NM_015702.2:c.307_324dup18')
In [8]: str(var_c)
Out[8]: 'NM_015702.2:c.307_324dup18'
In [9]: var_c = p2.parse_hgvs_variant('NC_000014.8:g.88401076_88459508copy4')
In [10]: str(var_c)
Out[10]: 'NC_000014.8:g.88401076_88459508copy4'
In [11]: var_g = p2.parse_hgvs_variant('NC_000014.8:g.88401076_88459508copy4')
In [12]: str(var_g)
Out[12]: 'NC_000014.8:g.88401076_88459508copy4'

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Original comment by Rudolph Rico (Bitbucket: rrico, GitHub: rrico):

Shockingly, the initial test implementation of extending the grammar seems to be working... should have a version ready today (famous last words).

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