update docs for -b and -C options

Update index.md

Add gene id to output

Merge pull request #132 from griffithlab/improved_compare_junctions

Fixes docker files
Improves stats script
Updates readthedocs

Merge pull request #103 from griffithlab/extract_params

0.5.1 doc update

Merge pull request #99 from griffithlab/fix_E_v2

Fix e v2

bump version to 0.4.2 for skip count fix

Update the cis-ase model

Fix bug in variants annotate

version 0.2.0