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ConsensusModel's can't really be instantiated #1352

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fnothaft opened this Issue Jan 18, 2017 · 0 comments

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fnothaft commented Jan 18, 2017

Their constructors are all package private. I think that's the right approach, but we should have a singleton class that creates them. I'll:

  • Make a singleton to create consensus models
  • Improve the known INDEL consensus model, because it needs a bit of TLC
  • Add functions for merging multiple consensus models

I need this for bigdatagenomics/avocado#200.

@fnothaft fnothaft added this to the 0.21.1 milestone Jan 18, 2017

@fnothaft fnothaft self-assigned this Jan 18, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Jan 19, 2017

[ADAM-1352] Clean up consensus model usage.
Resolves #1352:

* Fixed issues with consensus model instantiation.
* Added union consensus model (to support multiple models).
* Cleaned up consensus model documentation.
* Call distinct in IndelRealigner on consensus sequences to eliminate dupes.
* Added test for known indel model. Fixed off by one bug.
* Add test for union model.

fnothaft added a commit to fnothaft/adam that referenced this issue Jan 19, 2017

[ADAM-1352] Clean up consensus model usage.
Resolves #1352:

* Fixed issues with consensus model instantiation.
* Added union consensus model (to support multiple models).
* Cleaned up consensus model documentation.
* Call distinct in IndelRealigner on consensus sequences to eliminate dupes.
* Added test for known indel model. Fixed off by one bug.
* Add test for union model.

@heuermh heuermh closed this in #1357 Jan 19, 2017

heuermh added a commit that referenced this issue Jan 19, 2017

[ADAM-1352] Clean up consensus model usage.
Resolves #1352:

* Fixed issues with consensus model instantiation.
* Added union consensus model (to support multiple models).
* Cleaned up consensus model documentation.
* Call distinct in IndelRealigner on consensus sequences to eliminate dupes.
* Added test for known indel model. Fixed off by one bug.
* Add test for union model.
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