INFRA-541 Parse Cuppa arguments properly

Pull out only those arguments that are for each application based on
whether they have a prefix or not, then pass the appropriate ones to
each application in turn.

cuppa/src/main/java/com/hartwig/hmftools/cup/cli/PrepPlusPredictionMain.java

@@ -1,14 +1,41 @@
 package com.hartwig.hmftools.cup.cli;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
 import com.hartwig.hmftools.cup.prep.CuppaDataPrep;
 
 public class PrepPlusPredictionMain {
+    private static String[] extract(String prefix, String[] allArgs) {
+        List<String> allAsString = Arrays.stream(allArgs).collect(Collectors.toList());
+        List<String> matchingArgs = new ArrayList<>();
+        List<String> accumulator = new ArrayList<>();
+        String argPrefix = String.format("-%s_", prefix);
+        for (String arg: allAsString) {
+            if (arg.startsWith(argPrefix)) {
+                matchingArgs.addAll(accumulator);
+                accumulator.clear();
+                accumulator.add("-" + arg.substring(argPrefix.length()));
+            }
+            else {
+                if (!(arg.startsWith("-") || accumulator.isEmpty())) {
+                    accumulator.add(arg);
+                }
+            }
+        }
+        matchingArgs.addAll(accumulator);
+        return matchingArgs.toArray(new String[] {});
+    }
+
     public static void main(String[] args) {
         try {
-            CuppaDataPrep.main(args);
-            PredictionRunner.main(args);
+            CuppaDataPrep.main(extract("prep", args));
+            PredictionRunner.main(extract("prediction", args));
             System.exit(0);
         } catch (Exception e) {
+            System.err.println("Failed to run combined Cuppa applications");
             e.printStackTrace();
             System.exit(1);
         }