Squashing Commits;

Adding gitignore

All sandbox scripts are now executable

Ran a chmod +x *.py

sandbox scripts now conform to pep8

autopep8 --in-place was run

Added #! and copyright header

Trailing white space in a header line removed

Headers corrected/removed

a. Headers removed from upstream files
b. Headers corrected in files under khmer
c. Contact email removed from setup.py

gitignore updated

Years updated in all py scripts

Copyright years changed from 2009-2014 to 2009-2013 in all .py files

Copyright years updated in shell scripts

Copyright headers updated in all C++ and MATLAB files

Minor formatting bug fixes

White spaces added in header to ensure consistency

Copyright years updated based on git log

Headers corrected/removed

a. Headers removed from upstream files
b. Headers corrected in files under khmer
c. Contact email removed from setup.py

Years updated in all py scripts

Copyrght years changed from 2009-2014 to 2009-2013 in all .py files

Copyright years updated in shell scripts

Minor formatting bug fixes

White spaces added in header to ensure consistency

Copyright years updated based on git log