Lots of changes to maintain code coverage. Thanks chatGPT.

broadinstitute · Jan 15, 2025 · 7d1ff5f · 7d1ff5f
1 parent de9a1b9
commit 7d1ff5f
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Showing 2 changed files with 24 additions and 7 deletions.
diff --git a/src/java/org/broadinstitute/dropseqrna/utils/CompareBAMTagValues.java b/src/java/org/broadinstitute/dropseqrna/utils/CompareBAMTagValues.java
@@ -779,13 +779,6 @@ protected String[] customCommandLineValidation() {
 		if (TAG_VALUES_OUTPUT != null)
 			IOUtil.assertFileIsWritable(this.TAG_VALUES_OUTPUT);
 
-		if (useBaseCompression & useFixedLengthBaseCompression) {
-			list.add("Overriding the useBaseCompression flag with useFixedLengthBaseCompression flag.");
-			this.useBaseCompression=false;
-		}
-
-
-
 		return CustomCommandLineValidationHelper.makeValue(super.customCommandLineValidation(), list);
 	}
 

diff --git a/src/tests/java/org/broadinstitute/dropseqrna/utils/CompareBAMTagValuesTest.java b/src/tests/java/org/broadinstitute/dropseqrna/utils/CompareBAMTagValuesTest.java
@@ -17,6 +17,7 @@
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.assertNull;
 
 public class CompareBAMTagValuesTest {
 
@@ -196,4 +197,27 @@ public void testPairedReadOrderComparator_BothUnpaired() {
         assertEquals(result, 0, "Both unpaired reads should be considered equal");
     }
 
+    @Test
+    public void testCustomCommandLineValidation() {
+        CompareBAMTagValues compareBAMTagValues = new CompareBAMTagValues();
+
+        // Case 1: TAGS_1 and TAGS_2 length mismatch
+        compareBAMTagValues.TAGS_1 = Arrays.asList("CB", "CR");
+        compareBAMTagValues.TAGS_2 = Collections.singletonList("CB");
+        String[] validationResult = compareBAMTagValues.customCommandLineValidation();
+        assertEquals(validationResult.length, 1);
+        assertEquals(validationResult[0], "TAGS_1 and TAGS_2 must be the same length.");
+
+        // Case 2: Writable files
+        compareBAMTagValues.TAGS_1 = Arrays.asList("CB", "CR");
+        compareBAMTagValues.TAGS_2 = Arrays.asList("CB", "CR");
+        compareBAMTagValues.BAM_OUTPUT_1 = new File("test_output_1.bam");
+        compareBAMTagValues.BAM_OUTPUT_2 = new File("test_output_2.bam");
+        compareBAMTagValues.READ_COUNT_OUTPUT = new File("read_count_output.txt");
+        compareBAMTagValues.TAG_VALUES_OUTPUT = new File("tag_values_output.txt");
+        validationResult = compareBAMTagValues.customCommandLineValidation();
+        assertNull(validationResult);
+
+    }
+
 }