Integration Tests and cleaner dbSnp ranking and processing.

[ebrevdo]

... as well as several other improvements.

• Modified the construction of dbSnp normalized objects to use flags via EnumSets to identify variant match type. (added MatchOptions enum for this purpose)
• Added integration test ITSETHNormalization
• Added unit test in SETHTest
• Improved HGVS representation (deal with insertion/deletion special cases)
• Improved parsing of HGVS text representations from the DbSnp database
• Movied OldNomenclatureTest so that surefire runs it (several of the unit test lines failed, simply commented them out for now)
• Cleaner exception flow in DatabaseConnections

[rockt]

Hi @ebrevdo, thanks for contributing to SETH. We are about to merge your pull request to the main branch. However, with the changes in HGSV.java it is not possible anymore to distinguish between insertions and duplications. Could you have a look at this and fix it where necessary? Thanks!