Drop ref arg to sawfish

Author: bbimber

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

@@ -120,9 +120,6 @@ private File runSawfishCall(JobContext ctx, List<File> inputs, ReferenceGenome g
                 args.add(String.valueOf(maxThreads));
             }
 
-            args.add("--ref");
-            args.add(genome.getWorkingFastaFile().getPath());
-
             for (File sample : inputs)
             {
                 args.add("--sample");