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[ADAM-1242] Clean up dead code in org.bdgenomics.adam.util. #1243

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merged 3 commits into from Nov 7, 2016

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@fnothaft fnothaft commented Nov 5, 2016

Resolves #1242. Removed:

  • org.bdgenomics.adam.util.ImplicitJavaConversions
  • org.bdgenomics.adam.util.IntervalListReader
  • org.bdgenomics.adam.util.MapTools
  • org.bdgenomics.adam.util.RegExp
  • org.bdgenomics.adam.util.Util
Resolves #1242. Removed:

* org.bdgenomics.adam.util.ImplicitJavaConversions
* org.bdgenomics.adam.util.IntervalListReader
* org.bdgenomics.adam.util.MapTools
* org.bdgenomics.adam.util.RegExp
* org.bdgenomics.adam.util.Util
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@AmplabJenkins AmplabJenkins commented Nov 5, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1556/
Test PASSed.

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@fnothaft fnothaft commented Nov 6, 2016

I've added two commits:

  • 694dbe2 does a general documentation cleanup
  • f148b07 moves several classes/objects to different packages, and tightens up protections on these classes

This is good to go from my side.

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@AmplabJenkins AmplabJenkins commented Nov 6, 2016

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1557/
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case class ReferenceContigMap(contigMap: Map[String, Seq[NucleotideContigFragment]]) extends ReferenceFile {

// create sequence dictionary
/**
* The sequence dictionary corresponding to the contigs in this two bit file.

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@heuermh

heuermh Nov 7, 2016
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this isn't a two bit file

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@heuermh heuermh commented Nov 7, 2016

Looks great other than one doc fix

fnothaft added 2 commits Nov 6, 2016
…nup:

* Moved `NormalizationUtils` to `org.bdgenomics.adam.algorithms.consensus`, and
  made it package private to `consensus`.
* Moved `MdTag` to `org.bdgenomics.adam.models`.
* Moved `QualityScore` to `org.bdgenomics.adam.models` and made it package
  private to `consensus`.
@fnothaft fnothaft force-pushed the fnothaft:issues/1242-cleanup-util branch from f148b07 to bdf626c Nov 7, 2016
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@fnothaft fnothaft commented Nov 7, 2016

Fixed the documentation issue and pushed.

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@AmplabJenkins AmplabJenkins commented Nov 7, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1561/
Test PASSed.

@heuermh
heuermh approved these changes Nov 7, 2016
@heuermh heuermh merged commit 266e2fc into bigdatagenomics:master Nov 7, 2016
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@heuermh heuermh commented Nov 7, 2016

Thanks, @fnothaft!

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