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().
Making Chromosome.createIntergenicAnnotations private.
Adding some TODOs with things to talk about.
Merge pull request #25 from holtgrewe/feature/main_program_cleanup

Some more refactoring.