Updates to indel realigner to improve performance and accuracy.
Adding scripts for publishing scaladoc.
Merge pull request #319 from fnothaft/publish-scaladoc

Adding scripts for publishing scaladoc.
Remove extraneous implicit methods
Merge pull request #314 from fnothaft/indel-realigner-rebase

Updates to indel realigner to improve performance and accuracy.
Merge pull request #320 from genomebridge/remove-implicit-methods

Remove extraneous implicit methods in ReferenceMappingContext
Adding code for lifting over between sequences and the reference genome.