Documentation

(README)
remove all *.cov, *.bt2, *.sam files
Added a simple graphics module and added png output to clipper
Updated Documentation
Improved graphics

Can now write window-level images as well
Improved naming consistency
test case modifications
Possible off-by-one bug fix in SAM parser
Possible off-by-one bug fix in SAM parser
...
readded testfiles -.-
Final versions of our testcases for this milestone
Added Mike's practical test
Added Mike's practical test
Added Mike's practical test
Added Mike's practical test
Added Jason's common output implementation
clipper can now create its own output dir
added script for running practical tests
new practical tests
latest practical tests