Bugfix to bwamem2 index args

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAMem2Wrapper.java

@@ -42,6 +42,8 @@ public static class BWAMem2AlignmentStep extends BWAMemAlignmentStep
         public BWAMem2AlignmentStep(AlignmentStepProvider<?> provider, PipelineContext ctx)
         {
             super(provider, ctx, new BWAMem2Wrapper(ctx.getLogger()));
+
+            _addBtwswArg = false;
         }
     }
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAWrapper.java

@@ -41,7 +41,6 @@ public BWAWrapper(@Nullable Logger logger)
         super(logger);
     }
 
-
     public static class Provider extends AbstractAlignmentStepProvider<AlignmentStep>
     {
         public Provider()
@@ -83,6 +82,8 @@ public AlignmentStep create(PipelineContext context)
 
     public static class BWAAlignmentStep<WrapperType extends BWAWrapper> extends AbstractAlignmentPipelineStep<WrapperType> implements AlignmentStep
     {
+        protected boolean _addBtwswArg = true;
+
         public BWAAlignmentStep(AlignmentStepProvider provider, PipelineContext ctx, WrapperType wrapper)
         {
             super(provider, ctx, wrapper);
@@ -116,8 +117,11 @@ public IndexOutput createIndex(ReferenceGenome referenceGenome, File outputDir)
                 args.add("index");
 
                 //necessary for DBs larger than 2gb
-                args.add("-a");
-                args.add("bwtsw");
+                if (_addBtwswArg)
+                {
+                    args.add("-a");
+                    args.add("bwtsw");
+                }
 
                 args.add("-p");