Fixed line break after function.
Fixed indentation of purge function.
Added outfile to reformat() command so it can be used separately.
Changed outfile to outprefix, added it to circos_output as well
(easier to debug!)
Added logger, logging to debug why reordering by target is not working.
Fixed reformat of genomeCMP so that resorting by the taret genome
works.

This uses python instead of command line tools to process.
removed sortbytarget function, unused.
Use DictReader instead of file and mapping lambda function.
Fixed spacing issue.
Merge pull request #2 from kdaily/fixgenomecmp

Fix genomeCMP.py resorting by target genome