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Clean up CLI operation categories and names, and add documentation for CLI #1274

Merged
merged 1 commit into from
Nov 17, 2016
Merged

Clean up CLI operation categories and names, and add documentation for CLI #1274

merged 1 commit into from
Nov 17, 2016

Commits on Nov 17, 2016

  1. Clean up CLI operation categories and names, and add documentation fo… 

    …r CLI.

* Removed CalculateDepth command.
* Clean up argument doc in TransformFeatures.
* Move OUTPUT to an option for Flagstat.
* Remove some output saving arguments in the View command that don't exactly
  make sense.
* Remove unused Vcf2ADAM/ADAM2Vcf -dict option and
  `org.bdgenomics.adam.cli.DictionaryCommand` trait.
* Remove WigFix2ADAM command.
* Move away from ParquetLoadSaveArgs.
* Move reads2coverage to actions.
* Reads2Coverage does not only write to Parquet, so clean up docs.
* Clean up fragments<->reads argument names.
    @fnothaft
    fnothaft committed Nov 17, 2016
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