Funcotator can't handle variants that start outside an exon and end within an exon

[jonn-smith]

Funcotator must be able to handle indels that span exon start boundaries.

For example, in hg19 the following variant is not handled properly:

chr5:71622537-71622538 CA->C

The current workaround is to throw a FuncotatorUtils.TranscriptCodingSequenceException for the transcript causing this problem in Gencode.

[jonn-smith]

This is related to #4307

[droazen]

@jonn-smith I think you should close this issue in favor of #4307, since #4307 is a strict superset of this issue.

[jonn-smith]

OK - will do.