Using APPRIS tags during transcript selection

APPRIS tags are used in the transcript selection process.
See issue #231 for more info

Misc:
adding gencode19 datasources to testdata
adding a checking that ref AND alt don't both == "-" in infer_variant
wiring tx_mode option for gencode in TestUtils which currently didn't do anything
Please do.  Many thanks!

On Mon, Dec 8, 2014 at 10:50 AM, lbergelson <notifications@github.com>
wrote:

> In test/EnsemblTranscriptDatasourceTest.py:
>
> > @@ -189,7 +225,7 @@ def test_overlapping_gene_5flank(self):
> >
> >      def test_small_positive_strand_transcript_change(self):
> >          """Test one location on a transcript and make sure that the transcript change rendered properly """
> > -        ds = TestUtils._create_test_gencode_ds("out/small_positive_strand_")
> > +        ds = TestUtils._create_test_gencode_v18_ds("out/small_positive_strand_")
>
> I just kept them on v18 because I didn't want to change them. I can flip
> them to 19 and see if they still pass, which would be good because we could
> remove the 18 versions.
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/broadinstitute/oncotator/pull/255/files#r21461173>.
>



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Lee Lichtenstein
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