basic BamWindow wrapper
add super sketchy --options to take raw command line options sting ala DV2
get a plausible workflow
cleanup

clean up commented out cruft
add _filter_to_chromosome to facilitate the CopyCatSomaticWithBamWindow test
add a BamWindow test
make a real test for this tool
get a working version of CopyCatSomaticWithBamWindow and a test
remove unnecessary cruft
remove old nonsensiacal v1 test-data and move good v2 test data to v1
whitespace and formatting
stop hardcoding CopyCat/Somatic annotation directory. use the new software results
Use the copycat Annotation data software results
spin up a temporary annotation set in the test
switch to building a test annotation set in the test