Provide backwards compatible support for running some GATK 1.6 tools: recalibration still not supported. Generalize configuration retrieval and move into correct namespace
Improve assessment of callable regions: more identifcation and filtering of non-callable regions to final set of samples, allowing better spacing throughout a set of project samples
Avoid re-identifying analysis regions unless nblock files changes. Provides back compatibility for older approaches so updates do not change pre-existing analyses