Major changes (untested yet!)--
- Adding ability to do align+read quant without DGE analysis (for standard pipeline)
- Restructuring python script to prepare the alignments- more sensible class definitions now.  Also wraps the picard tools reference in a better location (instead of a sed
replace)
- Output report creation-- making more modular.  Relies on piecing together several templates to generate the reports.  Eliminates most code specific to each tabbed section of
output report.