Merge pull request #98 from cnobles/updates_v1.2.0

**v1.2.0**

* Updated build to R-base 4.4 (overdue) and rebuilt environment files.
* Due to the large jump in many package versions, minor modifications needed to be made the the software, making many changes incompatible with prior scripts.
* Special Note: ReadName patterns in configs need to be double escaped (ie. [\\\\w]). Please see simulation config files for examples.

Merge pull request #94 from cnobles/update_v1.1.2

Update v1.1.2

Fine tuning documentation changes.

Merge pull request #69 from cnobles/update_1.1.0

Update 1.1.0

Merge pull request #62 from cnobles/vc_incorp

Implement Version Control on IncorpData

Merge pull request #39 from cnobles/update_v0.9.9

Update v0.9.9

Updated readme and bug in table generation for reports.

Updated documentation and version to v0.9.7

Merge pull request #34 from cnobles/update_v0.9.6

* Introduced process workflow steps: assimilate and evaluate
  + Assimilate aligned data and compare with targeting sequences
    + Core data object that can be combined across runs / projects
  + Evaluated data incorporates reference data and statistical models
    + A staple data object for reports and can be constructed from multiple runs
* Included new subcommands 'eval' and modified 'report'
  + report from either config(s) or eval dataset
* Cleaned up file structure
* Updated documentation in code and docs.
* Implemented accuracy and retention checks with simulation dataset.
* Updated simulation dataset with larger set to test analysis.

Merge pull request #31 from cnobles/update_v0.9.5

Update v0.9.5