jibsch/Socrates — pull request #2 by arthurhsu3883 (2013-09-13 02:14:25+00:00)
Title: Debugged

Arthur's new version.

Fixed duplicated breakpoints.
Fixed cleaning up of temporary files.
Fixed exception handling.
Fixed single-end data bugs.

Updated the driver script:
1. got rid of intermediate shell driver script and is fully Pythonic.
2. JVM memory is as script option and performs a rough required memory check.
3. changes to subprocess calls that should take care of potential blocking of script.