Some more fixes to Jannovar.
Creating code for splitting of functionality into commands.
Supressing some warnings.
Somewhat at a dead end, we need to refactor the DuplicationAnnotationBuilder.
Several classes for easier genomic coordinate handling.

Includes tests.
First try on SNV annotation builder.
Changes that fixes problems in handling the reverse strand.
Some source code reformatting.
Adding types for CDS position and interval.
Using CDS Position in projection tests.
Introducing DuplicationChecker class.
Updating toString() of CDS and Transcript position/interval.
Enough preparation such that insertion annotation builder can be written.
Implementing insertion annotation builder.

Frame shift insertion where the affected codon is not the stop codon works.
More tests for the insertion annotation builder and some fixes.
First feature complete version of InsertionAnnotationBuilder.
Whitespace/comment changes.
Various updates.
Adding builder for HGVS positions.
More changes and helpers for coordinates and transcripts.