bug in examples/creating-a-variant.ipynb

[reece]

creating-a-variant.ipynb used to have:

var2 = copy.deepcopy(var)
var2.posedit.pos.end.uncertain=True
str(var2)

which resulted in

HGVSUnsupportedOperationError             Traceback (most recent call last)
<ipython-input-15-46125b6620a4> in <module>()
      1 var2 = copy.deepcopy(var)
      2 var2.posedit.pos.end.uncertain=True
----> 3 str(var2)

/home/reece/projects/biocommons/hgvs/hgvs/sequencevariant.py in format(self, conf)
     33         """
     34         if self.posedit is not None:
---> 35             posedit = self.posedit.format(conf)
     36         else:
     37             posedit = "?"

/home/reece/projects/biocommons/hgvs/hgvs/posedit.py in format(self, conf)
     27             rv = str(self.edit.format(conf))
     28         else:
---> 29             rv = "{pos}{edit}".format(pos=self.pos.format(conf), edit=self.edit.format(conf))
     30 
     31         if self.uncertain:

/home/reece/projects/biocommons/hgvs/hgvs/location.py in format(self, conf)
    313         if self.start is None:
    314             return ""
--> 315         if self.end is None or self.start == self.end:
    316             return self.start.format(conf)
    317         iv = self.start.format(conf) + "_" + self.end.format(conf)

/home/reece/projects/biocommons/hgvs/hgvs/location.py in __eq__(lhs, rhs)
    169         assert type(lhs) == type(rhs), "Cannot compare coordinates of different representations"
    170         if lhs.uncertain or rhs.uncertain:
--> 171             raise HGVSUnsupportedOperationError("Cannot compare coordinates of uncertain positions")
    172         return lhs.datum == rhs.datum and lhs.base == rhs.base and lhs.offset == rhs.offset
    173 

HGVSUnsupportedOperationError: Cannot compare coordinates of uncertain positions

Setting var2.posedit.pos.end.uncertain=True was removed in order to fix the notebook. We should restore it when the bug is fixed.