Fix BWA-Mem2 inheritance

BimberLab · Nov 27, 2024 · 9c0f8c2 · 9c0f8c2
1 parent a79c0ec
commit 9c0f8c2
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Showing 2 changed files with 7 additions and 8 deletions.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAMem2Wrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAMem2Wrapper.java
@@ -37,18 +37,12 @@ public BWAMem2Wrapper(@Nullable Logger logger)
         super(logger);
     }
 
-    public static class BWAMem2AlignmentStep extends BWAAlignmentStep<BWAMem2Wrapper>
+    public static class BWAMem2AlignmentStep extends BWAMemAlignmentStep
     {
         public BWAMem2AlignmentStep(AlignmentStepProvider<?> provider, PipelineContext ctx)
         {
             super(provider, ctx, new BWAMem2Wrapper(ctx.getLogger()));
         }
-
-        @Override
-        public boolean doAddReadGroups()
-        {
-            return false;
-        }
     }
 
     public static class Provider extends AbstractAlignmentStepProvider<AlignmentStep>

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAMemWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAMemWrapper.java
@@ -38,9 +38,14 @@ public BWAMemWrapper(@Nullable Logger logger)
 
     public static class BWAMemAlignmentStep extends BWAAlignmentStep<BWAMemWrapper>
     {
+        public BWAMemAlignmentStep(AlignmentStepProvider<?> provider, PipelineContext ctx, BWAMemWrapper wrapper)
+        {
+            super(provider, ctx, wrapper);
+        }
+
         public BWAMemAlignmentStep(AlignmentStepProvider<?> provider, PipelineContext ctx)
         {
-            super(provider, ctx, new BWAMemWrapper(ctx.getLogger()));
+            this(provider, ctx, new BWAMemWrapper(ctx.getLogger()));
         }
 
         @Override