Workingon generalizing quantify_exons.pl
Adding some comments to clarify logic
Working on script for extracting exons from rum index
Add script to filter a csv file
Add setup script
Ignore some files
Add __init__.py
Ignore some files
Working on new quantifyexons script
Add some comments to quantify_exons.pl
Add remove_ds
Add cigar2spans
Add bsearch_boundary
Add bsearch module
Use parsed version of cigar string from sam file
Add method for iterating over genes
Print exons in same format as RUM
Working on makefile for exon quant test
Merge branch 'merging'

Conflicts:
	.gitignore