Fix lofreq args

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/LofreqAnalysis.java

@@ -150,10 +150,10 @@ public File execute(File input, File outputVcf, File fasta, @Nullable Integer th
             args.add(fasta.getPath());
 
             args.add("-o");
-            args.add(input.getPath());
-
             args.add(outputVcf.getPath());
 
+            args.add(input.getPath());
+
             execute(args);
 
             if (!outputVcf.exists())