Fix #1

Make blockStarts be offset from chromStart
Fix a couple issues with RUM and GTF parsing
Close #3

Add --no-transcript option
Merge branch 'no-transcripts' into develop
Add --min-overlap option
Merge branch 'master' into develop
Set default of 1 for min-overlap
Use strandedness for exon
Add strandedness for transcripts
Fix a test
Use np.searchsorted
Keep list of new exons at each overlap range
Get rid of some extra SeqFeature construction
Merge branch 'optimize' into develop

Conflicts:
	prepade/quantify.py
	prepade/test/test_geneio.py
Optimize exon count accumulation a bit
Add comments and remove unused code
Validate strand in exon index
Make some changes to strand support

In ExonIndex, use 1 to mean +, - to mean minus, 0 to mean
stranded but unknown, and None to mean no strand.

Validate strand when adding to the index or querying it.
Support unknown strand
Add Greg's sam2mappingstats script