Drop unused bissnp code

bimberlabinternal · Jun 12, 2024 · c823024 · c823024
1 parent 8daa92a
commit c823024
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diff --git a/primeseq/src/org/labkey/primeseq/PrimeseqModule.java b/primeseq/src/org/labkey/primeseq/PrimeseqModule.java
@@ -32,8 +32,6 @@
 import org.labkey.api.view.WebPartFactory;
 import org.labkey.primeseq.analysis.CombineMethylationRatesHandler;
 import org.labkey.primeseq.analysis.MethylationRateComparisonHandler;
-import org.labkey.primeseq.pipeline.BisSnpGenotyperAnalysis;
-import org.labkey.primeseq.pipeline.BisSnpIndelRealignerStep;
 import org.labkey.primeseq.pipeline.BismarkWrapper;
 import org.labkey.primeseq.pipeline.BlastPipelineJobResourceAllocator;
 import org.labkey.primeseq.pipeline.ClusterMaintenanceTask;
@@ -114,9 +112,6 @@ public PipelineStartup()
                 SequencePipelineService.get().registerPipelineStep(new BismarkWrapper.Provider());
                 SequencePipelineService.get().registerPipelineStep(new BismarkWrapper.MethylationExtractorProvider());
 
-                SequencePipelineService.get().registerPipelineStep(new BisSnpIndelRealignerStep.Provider());
-                SequencePipelineService.get().registerPipelineStep(new BisSnpGenotyperAnalysis.Provider());
-
                 SequenceAnalysisService.get().registerFileHandler(new MethylationRateComparisonHandler());
                 SequenceAnalysisService.get().registerFileHandler(new CombineMethylationRatesHandler());
 

diff --git a/primeseq/src/org/labkey/primeseq/pipeline/AbstractBisSnpWrapper.java b/primeseq/src/org/labkey/primeseq/pipeline/AbstractBisSnpWrapper.java
diff --git a/primeseq/src/org/labkey/primeseq/pipeline/BisSnpGenotyperAnalysis.java b/primeseq/src/org/labkey/primeseq/pipeline/BisSnpGenotyperAnalysis.java
diff --git a/primeseq/src/org/labkey/primeseq/pipeline/BisSnpIndelRealignerStep.java b/primeseq/src/org/labkey/primeseq/pipeline/BisSnpIndelRealignerStep.java