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Finishing up the cleanup on org.bdgenomics.adam.rdd. #1264

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merged 1 commit into from
Nov 16, 2016
Merged

Finishing up the cleanup on org.bdgenomics.adam.rdd. #1264

merged 1 commit into from
Nov 16, 2016

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fnothaft
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  • Made MDTagging private to read. Exposed it through AlignmentRecordRDD.
    Cleaned up where it was used in Transform.
  • Made FlagStat and most related models private to read.
  • Made all read.recalibration and read.realignment classes private to
    package. Depending on the class, this varied from:
    • adam for classes that need to be registered with kryo
    • read for the core RealignIndels and BaseQualityRecalibrator engines
    • Their subpackage where possible.
  • Made class values for genomic partitioners as private as possible.
  • Added documentation to all InFormatters, InFormatterCompanions, and OutFormatters. Made the InFormatters package private with private constructors.
  • Added method/class level scaladoc where missing.
  • Moved org.bdgenomics.adam.cli.FlagStatSuite to org.bdgenomics.adam.read, along with the NA12878.sam test resource, which was otherwise unused in the adam-cli submodule.

@heuermh
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heuermh commented Nov 13, 2016

I may have asked elsewhere, it seems like the InFormatters and OutFormatters need to be publicly accessible, i.e.

https://github.com/heuermh/adam-snpeff/blob/master/src/main/scala/com/github/heuermh/adam/snpeff/AdamSnpEff.scala#L52

It may be that I'm not using them correctly here, in that they aren't really implicit if I have to explicitly instantiate them.

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1595/
Test PASSed.

@fnothaft
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The InFormatterCompanion and OutFormatter need to be public. The InFormatter has to be accessible from rdd, but it's constructor only has to be accessible from the companion.

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heuermh commented Nov 14, 2016

Thanks for the clarification. I'll take a closer look at the formatter docs and the rest of this pull request tomorrow morning.

heuermh
heuermh approved these changes Nov 14, 2016
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Looks good, thanks!

fnothaft added a commit to fnothaft/adam that referenced this pull request Nov 15, 2016
@fnothaft
[ADAM-1083] Cleaning up org.bdgenomics.adam.models.
2a31383 
Along with bigdatagenomics#1263 and bigdatagenomics#1264, this resolves bigdatagenomics#1083.

* Removing unused org.bdgenomics.adam.models.ReadBucket class.
* Move org.bdgenomics.adam.models.ReferencePositionPair and
  org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read
  and make package private.
* Clean up duplicated methods and methods that were incorrectly in companion
  singleton for SequenceDictionary and ReadGroupDictionary.
* Removed all SamReader references.
* Make writable file headers private to ADAM.
* Eliminated manual VCF parsing code in SnpTable.
* Cleaned up scaladoc for all classes and singleton objects.
* Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.
@fnothaft fnothaft mentioned this pull request Nov 15, 2016
Merged
fnothaft added a commit to fnothaft/adam that referenced this pull request Nov 15, 2016
@fnothaft
[ADAM-1083] Cleaning up org.bdgenomics.adam.models.
97e7c1e 
Along with bigdatagenomics#1263 and bigdatagenomics#1264, this resolves bigdatagenomics#1083.

* Removing unused org.bdgenomics.adam.models.ReadBucket class.
* Move org.bdgenomics.adam.models.ReferencePositionPair and
  org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read
  and make package private.
* Clean up duplicated methods and methods that were incorrectly in companion
  singleton for SequenceDictionary and ReadGroupDictionary.
* Removed all SamReader references.
* Make writable file headers private to ADAM.
* Eliminated manual VCF parsing code in SnpTable.
* Cleaned up scaladoc for all classes and singleton objects.
* Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.
@fnothaft
Finishing up the cleanup on org.bdgenomics.adam.rdd.
4063b29 
* Made `MDTagging` private to `read`. Exposed it through `AlignmentRecordRDD`.
  Cleaned up where it was used in `Transform`.
* Made `FlagStat` and most related models private to `read`.
* Made all `read.recalibration` and `read.realignment` classes private to
  package. Depending on the class, this varied from:
  * `adam` for classes that need to be registered with `kryo`
  * `read` for the core `RealignIndels` and `BaseQualityRecalibrator` engines
  * Their subpackage where possible.
* Made class values for genomic partitioners as private as possible.
* Added documentation to all `InFormatter`s, `InFormatterCompanion`s, and
  `OutFormatter`s. Made the `InFormatter`s package private with private
  constructors.
* Added method/class level scaladoc where missing.
* Moved `org.bdgenomics.adam.cli.FlagStatSuite` to `org.bdgenomics.adam.read`,
  along with the `NA12878.sam` test resource, which was otherwise unused in the
  `adam-cli` submodule.
fnothaft added a commit to fnothaft/adam that referenced this pull request Nov 15, 2016
@fnothaft
[ADAM-1083] Cleaning up org.bdgenomics.adam.models.
3fa50a9 
Along with bigdatagenomics#1263 and bigdatagenomics#1264, this resolves bigdatagenomics#1083.

* Removing unused org.bdgenomics.adam.models.ReadBucket class.
* Move org.bdgenomics.adam.models.ReferencePositionPair and
  org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read
  and make package private.
* Clean up duplicated methods and methods that were incorrectly in companion
  singleton for SequenceDictionary and ReadGroupDictionary.
* Removed all SamReader references.
* Make writable file headers private to ADAM.
* Eliminated manual VCF parsing code in SnpTable.
* Cleaned up scaladoc for all classes and singleton objects.
* Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.
@AmplabJenkins
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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1608/
Test PASSed.

@heuermh heuermh merged commit e929676 into bigdatagenomics:master Nov 16, 2016
@heuermh
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heuermh commented Nov 16, 2016

Thank you, @fnothaft!

fnothaft added a commit to fnothaft/adam that referenced this pull request Nov 16, 2016
@fnothaft
[ADAM-1083] Cleaning up org.bdgenomics.adam.models.
f87e6a2 
Along with bigdatagenomics#1263 and bigdatagenomics#1264, this resolves bigdatagenomics#1083.

* Removing unused org.bdgenomics.adam.models.ReadBucket class.
* Move org.bdgenomics.adam.models.ReferencePositionPair and
  org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read
  and make package private.
* Clean up duplicated methods and methods that were incorrectly in companion
  singleton for SequenceDictionary and ReadGroupDictionary.
* Removed all SamReader references.
* Make writable file headers private to ADAM.
* Eliminated manual VCF parsing code in SnpTable.
* Cleaned up scaladoc for all classes and singleton objects.
* Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.
fnothaft added a commit to fnothaft/adam that referenced this pull request Nov 16, 2016
@fnothaft
[ADAM-1083] Cleaning up org.bdgenomics.adam.models.
b49c900 
Along with bigdatagenomics#1263 and bigdatagenomics#1264, this resolves bigdatagenomics#1083.

* Removing unused org.bdgenomics.adam.models.ReadBucket class.
* Move org.bdgenomics.adam.models.ReferencePositionPair and
  org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read
  and make package private.
* Clean up duplicated methods and methods that were incorrectly in companion
  singleton for SequenceDictionary and ReadGroupDictionary.
* Removed all SamReader references.
* Make writable file headers private to ADAM.
* Eliminated manual VCF parsing code in SnpTable.
* Cleaned up scaladoc for all classes and singleton objects.
* Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.
heuermh pushed a commit that referenced this pull request Nov 16, 2016
@fnothaft @heuermh
[ADAM-1083] Cleaning up org.bdgenomics.adam.models.
c1b4b7d 
Along with #1263 and #1264, this resolves #1083.

* Removing unused org.bdgenomics.adam.models.ReadBucket class.
* Move org.bdgenomics.adam.models.ReferencePositionPair and
  org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read
  and make package private.
* Clean up duplicated methods and methods that were incorrectly in companion
  singleton for SequenceDictionary and ReadGroupDictionary.
* Removed all SamReader references.
* Make writable file headers private to ADAM.
* Eliminated manual VCF parsing code in SnpTable.
* Cleaned up scaladoc for all classes and singleton objects.
* Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.
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@fnothaft @heuermh @AmplabJenkins