Add --memory arg to king/plink2

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java

@@ -178,7 +178,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             boolean dropGenotypes = params.optBoolean("dropGenotypes", false);
             boolean useBcfTools = params.optBoolean("useBcfTools", false);
             boolean doNotRetainUnmapped = params.optBoolean("doNotRetainUnmapped", false);
-            if (doNotRetainUnmapped && !useBcfTools)
+            if (!doNotRetainUnmapped && !useBcfTools)
             {
                 ctx.getLogger().debug("Picard LiftoverVcf requires an output file for rejected sites, so setting doNotRetainUnmapped to true");
                 doNotRetainUnmapped = true;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java

@@ -131,6 +131,15 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
             plinkArgs.add(threads.toString());
         }
 
+        Integer maxRam = SequencePipelineService.get().getMaxRam();
+        if (maxRam != null)
+        {
+            plinkArgs.add("--memory");
+
+            maxRam = maxRam * 1000;
+            plinkArgs.add(String.valueOf(maxRam));
+        }
+
         List<String> plinkArgs1 = new ArrayList<>(plinkArgs);
         plinkArgs1.add("--make-bed");
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java

@@ -218,6 +218,15 @@ private void runBatch(File inputVCF, File outputDirectory, VariantProcessingStep
             args.add(SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger()).toString());
         }
 
+        Integer maxRam = SequencePipelineService.get().getMaxRam();
+        if (maxRam != null)
+        {
+            args.add("--memory");
+
+            maxRam = maxRam * 1000;
+            args.add(String.valueOf(maxRam));
+        }
+
         args.addAll(getClientCommandArgs());
 
         getWrapper().execute(args);