Clean up packages #1083

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fnothaft opened this Issue Jul 18, 2016 · 3 comments

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fnothaft commented Jul 18, 2016

Documentation and packaging cleanup for:

  • org.bdgenomics.adam.models
  • org.bdgenomics.adam.projections
  • org.bdgenomics.adam.rich see #1263
  • org.bdgenomics.adam.serialization
  • org.bdgenomics.adam.util
  • org.bdgenomics.adam.rdd classes not cleaned up in #1051

@fnothaft fnothaft added this to the 0.20.0 milestone Jul 18, 2016

@fnothaft fnothaft changed the title from Clean up `org.bdgenomics.adam.projections` package to Clean up packages Jul 18, 2016

@heuermh heuermh referenced this issue Jul 18, 2016

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Release ADAM version 0.20.0 #1048

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heuermh Jul 19, 2016

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

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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.

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fnothaft commented Jul 19, 2016

@heuermh heuermh modified the milestones: 0.20.0, 0.22.0, 0.21.0 Oct 13, 2016

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 15, 2016

[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
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`.

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 15, 2016

[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
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`.

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 15, 2016

[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
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`.

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 16, 2016

[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
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`.

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 16, 2016

[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
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`.

@heuermh heuermh closed this in #1267 Nov 16, 2016

heuermh added a commit that referenced this issue Nov 16, 2016

[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
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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