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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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ConsensusModel's can't really be instantiated #1352

fnothaft opened this issue Jan 18, 2017 · 0 comments
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enhancement
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0.22.0

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fnothaft commented Jan 18, 2017 •
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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
@fnothaft
[ADAM-1352] Clean up consensus model usage.
3258b7c 
Resolves bigdatagenomics#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 fnothaft mentioned this issue Jan 19, 2017
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fnothaft added a commit to fnothaft/adam that referenced this issue Jan 19, 2017
@fnothaft
[ADAM-1352] Clean up consensus model usage.
333e419 
Resolves bigdatagenomics#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 pushed a commit that referenced this issue Jan 19, 2017
@fnothaft @heuermh
[ADAM-1352] Clean up consensus model usage.
9d7b4a3 
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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