Fixed bcv plot pdf output

- Added in line of code to generate link to pdf output for bcd plot
Secondary factor feature added

- Added ability to use secondary factor for better statistical power,
cannot perform tests on secondary factor levels currently.
- Added ability for tool to handle sample annotation files that contain
more rows than count tables have columns.
- Added check to halt if classical tests are used when secondary factor
is specified.
- Added sample filter count output.
- Added highlighting option to only highlight down regulated or up
regulated tags.