RNA filtering: check that the *variant transcript* is expressed

[timodonnell]

Currently we just check that the transcript containing the variant is expressed. We should instead check that the variant itself is in the expressed transcript. We are seeing lots of cases where this more stringent filter would reject an epitope but not the less stringent.

This will probably require moving away from processing cufflinks output. Could use the read_evidence module in varcode instead.

[iskandr]

Related: #62