From ab140e28264490db11e517fb2e699771f87ec4cd Mon Sep 17 00:00:00 2001
From: Mark Fleharty <fleharty@users.noreply.github.com>
Date: Mon, 30 Sep 2019 13:57:56 -0400
Subject: [PATCH] Fixing up tests in MarkDuplicates so that tests with duplex
 UMIs are handled properly (#1404)

* Fixing up tests in MarkDuplicates so that tests with duplex UMIs are handled properly.
---
 .../MarkDuplicateWithMissingBarcodeTest.java          | 11 ++++++++++-
 .../picard/sam/markduplicates/MarkDuplicatesTest.java |  4 ++--
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/test/java/picard/sam/markduplicates/MarkDuplicateWithMissingBarcodeTest.java b/src/test/java/picard/sam/markduplicates/MarkDuplicateWithMissingBarcodeTest.java
index ea01e04bb6..e9b989b438 100644
--- a/src/test/java/picard/sam/markduplicates/MarkDuplicateWithMissingBarcodeTest.java
+++ b/src/test/java/picard/sam/markduplicates/MarkDuplicateWithMissingBarcodeTest.java
@@ -19,13 +19,22 @@ private class MarkDuplicatesWithMissingBarcodesTester extends MarkDuplicatesTest
         @Override
         public void runTest() {
             boolean hasRX = false;
+            boolean isDuplex = false;
             for (final String argument : this.getArgs()) {
                 if (argument.startsWith(getArgumentName())) {
                     hasRX = true;
                     break;
                 }
+                if (argument.startsWith("DUPLEX_UMI")) {
+                    isDuplex = true;
+                    break;
+                }
+            }
+
+            // Tests that specify the RX tag, or the DUPLEX_UMI argument should not be used with missing barcodes.
+            if (!hasRX && !isDuplex) {
+                addArg(getArgumentName() + "=" + getTagValue());
             }
-            if (!hasRX) addArg(getArgumentName() + "=" + getTagValue());
 
             super.runTest();
         }
diff --git a/src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java b/src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java
index 868a264069..f12654b587 100644
--- a/src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java
+++ b/src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java
@@ -311,7 +311,7 @@ public void testWithIndividualReadBarcodes() {
     }
 
     @DataProvider(name = "testDuplexUmiDataProvider")
-    private Object[][] testDuplexUmiDataProvider() {
+    public Object[][] testDuplexUmiDataProvider() {
         return new Object[][]{
                 {
                         // Test case where UMIs are not duplex, but are the same.
@@ -358,7 +358,7 @@ private Object[][] testDuplexUmiDataProvider() {
         };
     }
 
-    @Test(dataProvider = "testDuplexUmiDataProvider",enabled = false)
+    @Test(dataProvider = "testDuplexUmiDataProvider")
     public void testWithUMIs(final boolean duplexUmi, final List<String> UMIs, final List<Integer> alignmentStart1,
                              final List<Integer> alignmentStart2, final List<Boolean> isDuplicate,
                              final List<Boolean> isFirstNegativeStrand, final List<Boolean> isSecondNegativeStrand) {