Finishing HTSJDK integration.
Merge pull request #22 from holtgrewe/feature/htsjdk_integration

Finishing HTSJDK integration.
Introducing JannovarOptions object.
Refactoring the option parsing into CommandLineParser.
Merge pull request #23 from holtgrewe/feature/jannovar_program_cleanup

Some refactorization for the main program.
Refactorizing VCF/Jannovar output code.

Introducing abstract class AnnotatedVariantWriter and adding
implementations for writing VCF and Jannovar output.  This cleans up
the Jannovar class a bit more.
More cleanup of the Jannovar class.

Moving download code into DownloadManager classes.  This allows for
further slimming down of the main driver class and easier understanding
of the code.  Also, it should be easier to add/remove transcript data
sources.

The download manager classes could go into their own module.
Adding serialVersionUID to silence Eclipse.
Adding some comment to AnnotatedVariantWriter.
Adding TODO.
Fixing typo in function name searchBigIntervall => searchBigInterval.
Some whitespace/comment HTML changes in AnnotatedVariantFactory.
Minor comment changes in Chromosome.java.
Removing logically dead code and adding a small TODO for clarification.
Removing superflous try/catch block, method throws anyway.

Also, some minor updates and comments.
Extracting some format parameters in Chromosome.java.

Also adding a TODO for a tentative bug.
Adding annotation on AnotatedVariantFactory.
Making some functions private in Chromosome.
Refactoring Chromosome.revcom to DNAUtils.reverseComplement().
Merge pull request #24 from holtgrewe/feature/main_program_cleanup

More main program refactorization