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Next round of fixes for all 3 tools. Genetrack must use optparse rather

GREG VON KUSTER requested to merge ghv2/pughlab:master into master

than the more ideal argparse since Python 2.6 is supported. A few other misellaneous fixes for the other 2 tools. The Pugh lab's idx datatype now has Galaxy extension ssccidx - the IUC told me that the more generic idx would not be accepted.

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