EX-64 (cgates/kmeng): Started Normalize refactor; added
RecognizedVcfReader
EX-64(cgates kmeng): VcfReader now takes FileReader object to construct.
EX-64(kmeng): Quick update to normalize_test and normalize.py
EX-64(cgates/kmeng): Added tests to normalize.py.
EX-64(cgates/kmeng): Modifying Strelka to have its own normalize.py
functionality.
EX-64(kmeng): Normalize functionality migrated to Strelka. Varscan in
the middle of tests.
(kmeng): Merge remote-tracking branch 'origin/develop' into
refactor_normalize

Conflicts:
	jacquard/normalize.py
	test/normalize_test.py
EX-64(kmeng): Continued work on moving normalize.py functionality into
VarScan, building tests now.
EX-64(kmeng): Committing changes made to Varscan and Strelka tests for
more precise JQException testing
EX-64(kmeng): More edits to Varscan and Normalize.
EX-64(kmeng): More refactoring done in normalize.py.
EX-64(jebene/kmeng): Finished VarScan implementation, testing now.
EX-64 (jebene/kmeng) - altered output filename so that it preserves
input filename prefixes and suffixes