Dataflow BaseRecalibrator, local only

[jean-philippe-martin]

• DF_BaseRecalibrator tool, can be called from the command line. Same syntax as BaseRecalibrator.
• BaseRecalibrator's integration tests ported to this Dataflow version.
• Small changes to make types serializable.
• Note that this pull request is an intermediate step as it only works for local computations.

(this depends on PR#522)

[coveralls]

Coverage increased (+0.1%) to 71.63% when pulling 7172d13 on jp_DF_BaseRecalibrator into 244e994 on master.

[akiezun]

this method seems very long and complex for something that 'delegates to CalibrationTablesBuilder'

[jean-philippe-martin]

I can add that it also downloads the reference and prints statistics to the DF logs.

[akiezun]

this is pretty scary looking code and it's not tied with the dataflow 'walker' interface and so i'm assuming it's just a temporary step to putting all of this in and start refactoring. fine to live in the dev package for now. It will show up on the commandline though - maybe we need a way to hide those dev tools.
@droazen your turn

[coveralls]

Coverage increased (+0.07%) to 71.61% when pulling cfdaca8 on jp_DF_BaseRecalibrator into 578c579 on master.

[wbrockman]

This PR has been open 6 days - I'd love to see it resolved. Hoping that a 1:1 conversation David R & JP can resolve the remaining issues quickly.

[akiezun]

well, JP just pushed the code addressing the review last night. I'm looking at it now too. We're working under the assumption that all of this code is going to go through an overhaul anyway I guess.

[akiezun]

done with my review. looks fine for merge to dev. Once David+David put their code in and my MarkDups is in we need to restructure all of this.

[jean-philippe-martin]

Merging as soon as Travis gives the OK.

[coveralls]

Coverage increased (+0.06%) to 71.6% when pulling 2127685 on jp_DF_BaseRecalibrator into 578c579 on master.

[coveralls]

Coverage increased (+0.06%) to 71.6% when pulling 2127685 on jp_DF_BaseRecalibrator into 578c579 on master.