From bc7212128d5bf18745b8eadc84a326a0eb27fc82 Mon Sep 17 00:00:00 2001
From: Sana Shah <54493565+sanashah007@users.noreply.github.com>
Date: Thu, 22 Aug 2024 12:26:51 -0700
Subject: [PATCH] fix: arg names

---
 .../hellbender/tools/walkers/conversion/GtfToBed.java       | 6 +++---
 .../tools/walkers/conversion/GtfToBedIntegrationTest.java   | 2 +-
 2 files changed, 4 insertions(+), 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
index 23e0b833375..4bbfb90c19b 100644
--- 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/src/test/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBedIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBedIntegrationTest.java
index 4f4792ed668..08fc1c09ef6 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBedIntegrationTest.java
+++ b/src/test/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());