Deleted some unused genotyping code #6354
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@vruano You should take a look and see if any of these chagnes are going to conflict with your HMM changes. I know you changed many of those classes in your branch. |
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@davidbenjamin I saw a few things that could use additional cleanup. Seems sane though.
| @@ -389,15 +382,15 @@ else if (matchingStart.size() == 1) { | |||
| * Creates a UnifiedArgumentCollection with appropriate values filled in from the arguments in this walker | |||
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This comment still talks about UnifiedArgumentCollection
| @@ -10,15 +10,15 @@ | |||
| * used only by the HaplotypeCaller for its isActive() determination. Should not be used for | |||
| * any other purpose! | |||
| */ | |||
| public final class MinimalGenotypingEngine extends GenotypingEngine<UnifiedArgumentCollection> { | |||
| public final class MinimalGenotypingEngine extends GenotypingEngine<StandardCallerArgumentCollection> { | |||
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| /** | |||
| * Creates a new unified genotyping given the UG configuration parameters and the targeted set of samples | |||
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all these comments talk about the UG configuration which is confusing and outdated
| @@ -307,19 +307,18 @@ private void initializeSamples() { | |||
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| private void initializeActiveRegionEvaluationGenotyperEngine() { | |||
| // create a UAC but with the exactCallsLog = null, so we only output the log for the HC caller itself, if requested | |||
| @@ -495,7 +494,7 @@ public ActivityProfileState isActive( final AlignmentContext context, final Refe | |||
| // TODO: now that old qual is gone, do we still need this? | |||
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PR #6343 addressed it, so the TODO will be gone after rebasing.
| final UnifiedArgumentCollection uac = new UnifiedArgumentCollection(); | ||
| uac.genotypeArgs = new GenotypeCalculationArgumentCollection(); | ||
| final StandardCallerArgumentCollection standardArgs = new StandardCallerArgumentCollection(); | ||
| standardArgs.genotypeArgs = new GenotypeCalculationArgumentCollection(); |
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I don't think this needs to be set here anymore since it was just constructed with the same thing.
| uac.genotypeArgs = new GenotypeCalculationArgumentCollection(genotypeArgs); | ||
| return new MinimalGenotypingEngine(uac, SAMPLES); | ||
| final StandardCallerArgumentCollection standardArgs = new StandardCallerArgumentCollection(); | ||
| standardArgs.genotypeArgs = new GenotypeCalculationArgumentCollection(genotypeArgs); |
lbergelson
assigned davidbenjamin and davidangb and unassigned lbergelson, davidbenjamin and davidangb
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Woops, messed up assigning people to this pr. Sorry @davidangb |
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@lbergelson back to you |
@lbergelson This stuff is all dead code. Would you care to review?