Adding indel realignment transform. Composed of several steps:
- Targets for realignment are generated
- Realignment candidates are generated using Smith-Waterman
- If candidates lead to a sufficient improvement, reads are realigned
Adding first RealignerTarget tests and small bugfixes to RealignerTarget code
RealignTargets: Kryo issues and tests

Resolving Kryo issues, adding more tests and solving minor general
issues with the RealignmentTarget creation.
Fixing one warning in RealignIndels
Adding tests for IndelRealigner
Changes to Realignment, including adding more tests
IndelRealignmentTarget: one-off error and indel ordering/merging