Fix bug in `process_consequences` that was introduced when adding support for VEP without polyphen

[jkgoodrich]

This adds the following fixes to the current process_consequences:

• There are some things wrong with this part of the code:

      modifier = _csq_score(tc)
      flag_condition = (tc.lof == "HC") & (tc.lof_flags != "")
      modifier -= hl.if_else(flag_condition, flag_score, no_flag_score)
      modifier -= hl.if_else(tc.lof == "OS", 20, 0)
      modifier -= hl.if_else(tc.lof == "LC", 10, 0)

• I don't think it is supposed to have modifier = _csq_score(tc) since it's already handled by:

      tcl = tcl.map(
          lambda tc: tc.annotate(csq_score=_csq_score(tc) - _csq_score_modifier(tc))
      )

• Missingness of .lof and .lof_flags is not handled correctly
  • One problem is the same as the one mentioned for the original code
  • Another problem is that if .lof or .lof_flags is missing, flag_condition will be missing, and therefore csq_score will be missing.
  • Also, if (tc.lof == "HC") is False, then flag_condition evaluates to False, so the no_flag_score will be subtracted from the modifier. This should only happen if (tc.lof == "HC") is True.

The updated function also has the following fixes to the original code (before the support for no polyphen was added):

• Allow lof_flags to be missing in addition to lof_flags == "" for lof == "HC" to have no flag penalty (note that this is a change from previous loftee annotations)
• Pass csq_order to add_most_severe_consequence_to_consequence (in the default case this wouldn't have caused an issue)

Here are some tests showing the comparison of the original code, the current code, and the code in this PR

fixes_to_process_consequences_small.html.zip

[jkgoodrich]

Yeah, my next PR completely changes this function, but it will take more time to review, so just getting this in with minimal changes to fix the bug. These changes were my first round of changes to fix the function before I got completely confused by this and other functions in vep.py and completely rewrote it

[mike-w-wilson]

Thank you!