fix: arg names

broadinstitute · Aug 22, 2024 · bc72121 · bc72121
1 parent ebaf095
commit bc72121
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java
@@ -78,8 +78,8 @@
 @DocumentedFeature
 @WorkflowProperties
 public class GtfToBed extends FeatureWalker<GencodeGtfFeature> {
-    public static final String SORT_BY_TRANSCRIPT_LONG_NAME = "sort-transcript";
-    public static final String SORT_BY_BASIC_LONG_NAME = "sort-basic";
+    public static final String SORT_BY_TRANSCRIPT_LONG_NAME = "sort-by-transcript";
+    public static final String USE_BASIC_TRANSCRIPT_LONG_NAME = "use-basic-transcript";
     public static final String INPUT_LONG_NAME = "gtf-path";
     protected final Logger logger = LogManager.getLogger(this.getClass());
 
@@ -92,7 +92,7 @@ public class GtfToBed extends FeatureWalker<GencodeGtfFeature> {
     @Argument(fullName = SORT_BY_TRANSCRIPT_LONG_NAME, doc = "Make each row of BED file sorted by transcript", optional = true)
     public boolean sortByTranscript = false;
 
-    @Argument(fullName = SORT_BY_BASIC_LONG_NAME, doc = "Only use basic transcripts")
+    @Argument(fullName = USE_BASIC_TRANSCRIPT_LONG_NAME, doc = "Only use basic transcripts")
     public boolean sortByBasic = false;
 
     //stores either gene or transcript ID and summary information about the feature

diff --git a/.../java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBedIntegrationTest.java b/.../java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBedIntegrationTest.java
@@ -66,7 +66,7 @@ public void testGtfToBed(GtfToBedTest params) throws IOException {
         args.add(new File (params.SD).getAbsolutePath());
         args.add("--" + GtfToBed.SORT_BY_TRANSCRIPT_LONG_NAME);
         args.add(params.transcript);
-        args.add("--" + GtfToBed.SORT_BY_BASIC_LONG_NAME);
+        args.add("--" + GtfToBed.USE_BASIC_TRANSCRIPT_LONG_NAME);
         args.add(params.basic);
         args.add("--" + StandardArgumentDefinitions.OUTPUT_LONG_NAME);
         args.add(outputFile.getAbsolutePath());