relationship between these two classes needs to be rethought; see JIRA
GSA-207.
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The whole GenotypeCall framework needs to be changed, but this will work for the time being.
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-Don't print verbose/debugging output to logger, but instead specify a file in the argument collection (and then we only need to print conditionally)
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-Allow walkers calling the UG to pass in their own argument collections
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Because it doesn't actually use EM, it's no longer a subclass of the EM model.
Note that you can't use it just yet because it doesn't actually emit calls (just prints to logger). I need to deal with general UG output tomorrow. Hold off until then, Mark, and then you can go wild.
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Chris, if this breaks an integration test, you get it.
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@PoolUtils - split reads by indel/simple base
@BaseTransitionTable - complete refactoring, nicer now
@UnifiedArgumentCollection - added PoolSize as an argument
@UnifiedGenotyper - checks to ensure pooled sequencing uses the appropriate model
@GenotypeCalculationModel - instantiates with the new PoolSize argument
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Also moved a buch of Lists over to Sets for consistancy.
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also: their, I hope your happy Eric, from now on I'll try not to flout my awesomest grammer in the future accept when I need to illicit a strong response :-)
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We need to filter contexts in that case since the calling walkers don't get UG's traversal-level filters.
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-Add another filter for read groups for Chris
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Remove all sequenom stuff from the FastaAlternateReferenceMaker so it can just concentrate on making alternate references...
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We currently get identical lods and slods as MultiSampleCaller (except slods for ref calls, as I discussed with Jared) and are a bit faster in my few test cases. Single-sample mode still emulates SSG.
The remaining to do items:
1. more testing still needed
2. we currently only output lods/slods, but I need to emit actual calls
3. stubs are in place for Mark's proposed version of the EM calculation and now I need to add the actual code.
More check-ins coming soon...
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For now, a single sample input will be special-cased in the EM model - but that will change when the EM model degenerates to the single sample output with a single sample as input. For now, the EM code for multi-samples isn't finished; I'm planning on checking that in soon.
The SingleSampleIntegrationTest now uses the UnifiedCaller instead of SSG, and so should all of you. More on that in a separate email.
Other minor cleanups added too.
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aaron
depristo
hanna
ebanks
asivache
chartl
andrewk
kiran