Fix a test
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
Add some logging
Merge branch 'develop' of github.com:itmat/pre-pade into develop
Speed up exon index creation a bit
Working on C impl of gene index
Working on exon index
Add search_exon (commented)
Split geneindex into two files
Get rid of ExonEvent
Add test program
Working on test framework
Add some tests
Add search_exons function