Working on transcript hit function
Add test
Add some tests
Change comapare_aln_to_transcript to take array
Take exons as array
Convert arra input to ndarray
Simplify tests
Report on exon hits
Disqualify any reads that hit an intron
Remove fields from TranscriptMatch
Fix comparison of read gaps and introns
Add some tests
Differentiate between a rejection and a no-decision

If we don't get any overlap, but the read doesn't actually
conflict with the transcript, don't decide false, decide None.
Add function for comparing paired reads
Working on integrating transcript quant
Fix field name
Use exon id in output
Make exon id from gene file
Use transcript index for exons, when we have it
Add ExonReadCounter