Merge pull request #1 from gpratt/master

Last update of gpratt/gscripts, moving to yeolab
added count_aligned_from_sam.py, does the same thing as perl script, except documented
added install script for aligned_reads_sam
fixed a count aligned bug and comitting half working a clipseq analysis for local testing
half way through refactoring, moving to local machine so I have better debugging
added (annotation free) version of count RPKM
Merge pull request #1 from YeoLab/rna_seq_edits

Rna seq edits