INFRA-541 Fix arg parsing corner case

hartwigmedical · Sep 6, 2024 · 30e8db4 · 30e8db4
1 parent a8a33cf
commit 30e8db4
Showing 1 changed file with 7 additions and 2 deletions.
diff --git a/cuppa/src/main/java/com/hartwig/hmftools/cup/cli/PrepPlusPredictionMain.java b/cuppa/src/main/java/com/hartwig/hmftools/cup/cli/PrepPlusPredictionMain.java
@@ -20,8 +20,13 @@ private static String[] extractArgs(String prefix, String[] allArgs) {
                 accumulator.add("-" + arg.substring(argPrefix.length()));
             }
             else {
-                if (!(arg.startsWith("-") || accumulator.isEmpty())) {
-                    accumulator.add(arg);
+                if (arg.startsWith("-")) {
+                    matchingArgs.addAll(accumulator);
+                    accumulator.clear();
+                } else {
+                    if (!accumulator.isEmpty()) {
+                        accumulator.add(arg);
+                    }
                 }
             }
         }