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Clean up Rich records #577

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fnothaft opened this Issue Feb 9, 2015 · 0 comments

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@fnothaft
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fnothaft commented Feb 9, 2015

A few things we discussed a while back:

  • Merge RichAlignmentRecord vs. DecadentRead
  • Remove per-record implicits
  • Add RDD level implicits
  • Remove RichVariant

@fnothaft fnothaft added this to the 0.17.0 milestone Mar 1, 2015

@fnothaft fnothaft modified the milestones: 0.18.0, 0.17.0 May 31, 2015

@fnothaft fnothaft modified the milestones: 1.0.0, 0.17.1 Aug 20, 2015

@heuermh heuermh added this to Triage in Release 1.0.0 Mar 8, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Mar 14, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Mar 14, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Mar 14, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Mar 15, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Mar 20, 2017

[ADAM-1358] Refactor BQSR to improve performance and legibility.
Resolves #1358.

* Adds instrumentation to BQSR.
* Changed SnpTable to remove RichVariant conversion, use VariantRDD API.
* Refactoring SnpTable to eliminate per-residue costly masked site lookup.
* Restructuring core of SnpTable around an array to improve GC performance.
  Additionally, wrote custom serializer to improve serialization performance.
* Added test suite for SnpTable, to test table creation.
* Refactored SnpTable to use an IntervalArray-like approach. This approach
  improves masked site lookup performance by 50%.
* Added tests to SnpTableSuite to cover lookup case, and reenabled tests in
  BaseQualityRecalibrationSuite.
* Adding unit test coverage to covariates
* Revert "[ADAM-775] Allow all IUPAC codes in BQSR"
  This reverts commit 207eeba.
* Pulled Seq allocation for base check out into an immutable set.
* Rewrote dinuc covariate. 50% improvement in performance.
* Rewrite main BQSR aggregate as reduce by key
* Added tests to recalibrator, recalibration table.
* Majorly refactors of BQSR tables.
* Starting to factor out the QualityScore class
* Refactoring CovariateKey to reduce size in memory
* Eliminated `org.bdgenomics.adam.rich.DecadentRead` (partially resolves #577)
* Refactor CovariateKey to store record group ID instead of record group name.
* Removed `org.bdgenomics.adam.models.QualityScore`.
* Split multi-class files into one class per file (excepting private classes) to improve navigability.
* Scaladoc all the recalibrators! You get a scaladoc! And you get a scaladoc!

fnothaft added a commit to fnothaft/adam that referenced this issue Mar 20, 2017

[ADAM-1358] Refactor BQSR to improve performance and legibility.
Resolves #1358.

* Adds instrumentation to BQSR.
* Changed SnpTable to remove RichVariant conversion, use VariantRDD API.
* Refactoring SnpTable to eliminate per-residue costly masked site lookup.
* Restructuring core of SnpTable around an array to improve GC performance.
  Additionally, wrote custom serializer to improve serialization performance.
* Added test suite for SnpTable, to test table creation.
* Refactored SnpTable to use an IntervalArray-like approach. This approach
  improves masked site lookup performance by 50%.
* Added tests to SnpTableSuite to cover lookup case, and reenabled tests in
  BaseQualityRecalibrationSuite.
* Adding unit test coverage to covariates
* Revert "[ADAM-775] Allow all IUPAC codes in BQSR"
  This reverts commit 207eeba.
* Pulled Seq allocation for base check out into an immutable set.
* Rewrote dinuc covariate. 50% improvement in performance.
* Rewrite main BQSR aggregate as reduce by key
* Added tests to recalibrator, recalibration table.
* Majorly refactors of BQSR tables.
* Starting to factor out the QualityScore class
* Refactoring CovariateKey to reduce size in memory
* Eliminated `org.bdgenomics.adam.rich.DecadentRead` (partially resolves #577)
* Refactor CovariateKey to store record group ID instead of record group name.
* Removed `org.bdgenomics.adam.models.QualityScore`.
* Split multi-class files into one class per file (excepting private classes) to improve navigability.
* Scaladoc all the recalibrators! You get a scaladoc! And you get a scaladoc!

@heuermh heuermh closed this in b1fce67 Mar 20, 2017

@heuermh heuermh moved this from Triage to Completed in Release 1.0.0 Mar 21, 2017

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