From 4c573e077848703c1f59e9c1e809455a20333406 Mon Sep 17 00:00:00 2001
From: Sana Shah <54493565+sanashah007@users.noreply.github.com>
Date: Mon, 26 Aug 2024 12:08:18 -0700
Subject: [PATCH] add: dictionary exception and corresponding test

---
 .../tools/walkers/conversion/GtfToBed.java    | 16 ++++++++++++----
 .../conversion/GtfToBedIntegrationTest.java   | 19 +++++++++++++++++++
 2 files changed, 31 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 272d27b55b5..656b815af6d 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
@@ -51,7 +51,7 @@
  * <pre>
  *     java -jar GtfToBed.jar \
  *     -gtf-path input.gtf \
- *     -sequence-dictionary dictionary.dict \
+ *     -R dictionary.dict \
  *     -sort-transcript \
  *     -output output.bed \
  * </pre>
@@ -98,6 +98,9 @@ public class GtfToBed extends FeatureWalker<GencodeGtfFeature> {
     //stores either gene or transcript ID and summary information about the feature
     private final Map<String, GtfInfo> featureInfoMap = new HashMap<>();
 
+    //Sequence dictionary
+    private SAMSequenceDictionary sequenceDictionary = null;
+
     @Override
     protected boolean isAcceptableFeatureType(Class<? extends Feature> featureType) {
         return featureType.isAssignableFrom(GencodeGtfFeature.class);
@@ -205,12 +208,17 @@ private void updateGeneInterval(GencodeGtfFeature gtfFeature, int geneStart, int
         featureInfoMap.put(gtfFeature.getGeneId(), gtfGeneInfo);
     }
 
+    @Override
+    public void onTraversalStart() {
+        sequenceDictionary = getBestAvailableSequenceDictionary();
+        if(sequenceDictionary == null){
+            throw new GATKException("Sequence Dictionary must be specified (" + StandardArgumentDefinitions.SEQUENCE_DICTIONARY_NAME + ").");
+        }
+    }
+
     // runs immediately after it has gone through each line of gtf (apply method)
     @Override
     public Object onTraversalSuccess() {
-        // get dictionary
-        SAMSequenceDictionary sequenceDictionary = getBestAvailableSequenceDictionary();
-
         // create linked hash map to store sorted values of idToInfo
         LinkedHashMap<String, GtfInfo> karyotypeIdToInfo = getSortedMap(sequenceDictionary);
 
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 08fc1c09ef6..ef6af2402a9 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
@@ -2,6 +2,7 @@
 
 import org.broadinstitute.hellbender.CommandLineProgramTest;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.exceptions.GATKException;
 import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -25,6 +26,7 @@ public class GtfToBedIntegrationTest extends CommandLineProgramTest {
     private static final String expectedNotBasicBed = ConversionTestUtils.getNotBasicBed();
     private static final String expectedMouseBed = ConversionTestUtils.getMouseBed();
 
+
     private static class GtfToBedTest {
         final String input;
         final String SD;
@@ -75,4 +77,21 @@ public void testGtfToBed(GtfToBedTest params) throws IOException {
 
         IntegrationTestSpec.assertEqualTextFiles(new File(params.expected), outputFile);
     }
+
+    @Test(expectedExceptions = GATKException.class)
+    public void testGtfToBedNoSequenceDictionary() {
+        final File outputFile = createTempFile("outputBed", ".bed");
+        final ArrayList<String> args = new ArrayList<>();
+
+        args.add("--" + GtfToBed.INPUT_LONG_NAME);
+        args.add(new File (mapk1).getAbsolutePath());
+        args.add("--" + GtfToBed.SORT_BY_TRANSCRIPT_LONG_NAME);
+        args.add(String.valueOf(true));
+        args.add("--" + GtfToBed.USE_BASIC_TRANSCRIPT_LONG_NAME);
+        args.add(String.valueOf(true));
+        args.add("--" + StandardArgumentDefinitions.OUTPUT_LONG_NAME);
+        args.add(outputFile.getAbsolutePath());
+
+        runCommandLine(args);
+    }
 }