added command line checker, logger, removed all ipython dependencies
added new python file
-added commmand line parsing/checking
-added a '-p' option which allows the pipeline to be started at a specified program
-added a logging function which records all stdout/stderr to a file based on the start time of the script
-removed all ipython dependencies to make this script more in line with the others
:
added verbose mode which enables script debug output
Modified README to include changes to SRAtoVCF.py