Update samtools merge argument order

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/SamtoolsMerger.java

@@ -25,8 +25,6 @@ public File mergeBams(List<File> inputBams, File outputFile) throws PipelineJobE
         List<String> params = new ArrayList<>();
         params.add(getSamtoolsPath().getPath());
         params.add(COMMAND);
-        params.add("-o");
-        params.add(outputFile.getPath());
 
         Integer threads = SequencePipelineService.get().getMaxThreads(getLogger());
         if (threads != null)
@@ -35,6 +33,9 @@ public File mergeBams(List<File> inputBams, File outputFile) throws PipelineJobE
             params.add(String.valueOf(threads));
         }
 
+        params.add("-o");
+        params.add(outputFile.getPath());
+
         inputBams.forEach(f -> params.add(f.getPath()));
 
         execute(params);