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Clean up packages #1083

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6 tasks done
fnothaft opened this issue Jul 18, 2016 · 3 comments · Fixed by #1267
Closed
6 tasks done

Clean up packages #1083

fnothaft opened this issue Jul 18, 2016 · 3 comments · Fixed by #1267
Milestone
0.21.0

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@fnothaft
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fnothaft commented Jul 18, 2016 •
edited by heuermh
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Documentation and packaging cleanup for:
@fnothaft fnothaft added this to the 0.20.0 milestone Jul 18, 2016
@fnothaft fnothaft changed the title Clean up org.bdgenomics.adam.projections package Clean up packages Jul 18, 2016
@heuermh heuermh mentioned this issue Jul 18, 2016
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@heuermh
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heuermh commented Jul 19, 2016

I'd like to propose the following package name changes:

org.bdgenomics.adam.rdd.features --> org.bdgenomics.adam.feature
org.bdgenomics.adam.rdd.variation --> org.bdgenomics.adam.variant

@heuermh
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heuermh commented Jul 19, 2016

object Timers in package org.bdgenomics.adam.instrumentation could use some higher level doc, when to define one, how to use one, etc.

@fnothaft
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+1 @heuermh

@heuermh heuermh modified the milestones: 0.20.0, 0.22.0, 0.21.0 Oct 13, 2016
@fnothaft fnothaft mentioned this issue Oct 14, 2016
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@fnothaft fnothaft mentioned this issue Nov 8, 2016
Merged
@heuermh heuermh mentioned this issue Nov 10, 2016
Merged
@fnothaft fnothaft mentioned this issue Nov 12, 2016
Merged
fnothaft added a commit to fnothaft/adam that referenced this issue 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 issue Nov 15, 2016
Merged
fnothaft added a commit to fnothaft/adam that referenced this issue 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 added a commit to fnothaft/adam that referenced this issue 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`.
@heuermh heuermh mentioned this issue Nov 16, 2016
Merged
fnothaft added a commit to fnothaft/adam that referenced this issue 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 issue 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 issue 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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[ADAM-1083] Cleaning up org.bdgenomics.adam.models. fnothaft/adam
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@heuermh @fnothaft