fix: use IntegrationTestSpec.assertEqualTextFiles()

broadinstitute · Aug 9, 2024 · e7ea45f · e7ea45f
1 parent 33dd8ea
commit e7ea45f
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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
@@ -40,7 +40,7 @@
  * <pre>
  *     java -jar GtfToBed.jar \
  *     -gtf-path input.gtf \
- *     -gtf-sequence-dictionary dictionary.dict \
+ *     -gtf-dictionary dictionary.dict \
 = *    -output output.bed \
  * </pre>
  *
@@ -50,8 +50,8 @@
  * <pre>
  *     java -jar GtfToBed.jar \
  *     -gtf-path input.gtf \
- *     -gtf-sequence-dictionary dictionary.dict \
- *     -sort-by-transcript \
+ *     -gtf-dictionary dictionary.dict \
+ *     -sort-transcript \
  *     -output output.bed \
  * </pre>
  *
@@ -61,9 +61,9 @@
  *  * <pre>
  *     java -jar GtfToBed.jar \
  *     -gtf-path input.gtf \
- *     -gtf-sequence-dictionary dictionary.dict \
- *     -sort-by-transcript \
- *     -sort-by-basic \
+ *     -gtf-dictionary dictionary.dict \
+ *     -sort-transcript \
+ *     -sort-basic \
  *     -output output.bed \
  *  * </pre>
  */
@@ -75,9 +75,9 @@
 )
 
 public class GtfToBed extends FeatureWalker<GencodeGtfFeature> {
-    public static final String SORT_BY_TRANSCRIPT_LONG_NAME = "sort-by-transcript";
-    public static final String SEQUENCE_DICTIONARY_LONG_NAME = "gtf-sequence-dictionary";
-    public static final String SORT_BY_BASIC_LONG_NAME = "sort-by-basic";
+    public static final String SORT_BY_TRANSCRIPT_LONG_NAME = "sort-transcript";
+    public static final String SEQUENCE_DICTIONARY_LONG_NAME = "gtf-dictionary";
+    public static final String SORT_BY_BASIC_LONG_NAME = "sort-basic";
     public static final String INPUT_LONG_NAME = "gtf-path";
 
 
@@ -126,7 +126,7 @@ private void processFeature(GencodeGtfFeature gtfFeature) {
         }
 
         //  check if the gtf feature is a transcript. If user only wants basic transcripts check that it has the basic tag
-        if (gtfFeature.getFeatureType() == GencodeGtfFeature.FeatureType.TRANSCRIPT) {
+        else if (gtfFeature.getFeatureType() == GencodeGtfFeature.FeatureType.TRANSCRIPT) {
             if (sortByBasic) {
                 for (GencodeGtfFeature.OptionalField<?> field : optionalFields) {
                     if ("basic".equals(field.getValue())) {

diff --git a/...test/java/org/broadinstitute/hellbender/tools/walkers/conversion/ConversionTestUtils.java b/...test/java/org/broadinstitute/hellbender/tools/walkers/conversion/ConversionTestUtils.java
@@ -24,6 +24,10 @@ public static String getReferenceDict(){
         return getTestDataDir()+"/reference.dict";
     }
 
+//    public static String getReferenceDict(){
+//        return GATKBaseTest.publicTestDir + "large/Homo_sapiens_assembly38.dict";
+//    }
+
     public static String getDecoySamplesGeneBed(){
         return getTestDataDir() + "/decoySampleGene.bed";
     }

diff --git a/.../java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBedIntegrationTest.java b/.../java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBedIntegrationTest.java
@@ -3,6 +3,7 @@
 import org.broadinstitute.hellbender.CommandLineProgramTest;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
+import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
@@ -109,10 +110,10 @@ private void runMapk1(boolean transcript) throws IOException {
 
         if (transcript) {
             Assert.assertEquals(countLines(outputFile), 3);
-            Assert.assertTrue(compareFiles(mapk1TranscriptBed, outputFile));
+            IntegrationTestSpec.assertEqualTextFiles(mapk1TranscriptBed, outputFile);
         } else {
             Assert.assertEquals(countLines(outputFile), 1);
-            Assert.assertTrue(compareFiles(mapk1GeneBed, outputFile));
+            IntegrationTestSpec.assertEqualTextFiles(mapk1GeneBed, outputFile);
         }
     }
 
@@ -128,11 +129,11 @@ private void runDecoySample(boolean transcript) throws IOException {
 
         if (transcript) {
             Assert.assertEquals(countLines(outputFile), 20);
-            Assert.assertTrue(compareFiles(decoysTranscriptBed, outputFile));
+            IntegrationTestSpec.assertEqualTextFiles(decoysTranscriptBed, outputFile);
 
         } else {
             Assert.assertEquals(countLines(outputFile), 19);
-            Assert.assertTrue(compareFiles(decoysGeneBed, outputFile));
+            IntegrationTestSpec.assertEqualTextFiles(decoysGeneBed, outputFile);
         }
     }
 
@@ -144,7 +145,7 @@ private void runManyTranscripts() throws IOException {
                 .add(GtfToBed.SORT_BY_BASIC_LONG_NAME, true)
                 .addOutput(outputFile);
         runCommandLine(argsBuilder);
-        Assert.assertTrue(compareFiles( manyTranscriptsBed, outputFile));
+        IntegrationTestSpec.assertEqualTextFiles(manyTranscriptsBed, outputFile);
 
     }
 
@@ -156,7 +157,7 @@ private void runNotBasic() throws IOException {
                 .add(GtfToBed.SORT_BY_BASIC_LONG_NAME, false)
                 .addOutput(outputFile);
         runCommandLine(argsBuilder);
-        Assert.assertTrue(compareFiles(notBasicBed, outputFile));
+        IntegrationTestSpec.assertEqualTextFiles(notBasicBed, outputFile);
     }
 
     private void runMouse() throws IOException {
@@ -167,7 +168,7 @@ private void runMouse() throws IOException {
                 .add(GtfToBed.SORT_BY_BASIC_LONG_NAME, false)
                 .addOutput(outputFile);
         runCommandLine(argsBuilder);
-        Assert.assertTrue(compareFiles(mouseBed, outputFile));
+        IntegrationTestSpec.assertEqualTextFiles(mouseBed, outputFile);
     }
 
     private int countLines(File file) throws IOException {
@@ -178,31 +179,4 @@ private int countLines(File file) throws IOException {
         }
         return lines;
     }
-
-    private boolean compareFiles(File file1, File file2) throws IOException {
-        BufferedReader reader1 = new BufferedReader(new FileReader(file1));
-        BufferedReader reader2 = new BufferedReader(new FileReader(file2));
-
-        String line1 = reader1.readLine();
-        String line2 = reader2.readLine();
-        int lineNum = 1;
-
-        while (line1 != null || line2 != null) {
-            if (line1 == null || line2 == null) {
-                System.out.println("File are different lengths");
-                return false;
-            } else if (!line1.equals(line2)) {
-                System.out.println("Difference at line " + lineNum);
-                System.out.println("File1: " + line1);
-                System.out.println("File2: " + line2);
-                return false;
-            }
-            line1 = reader1.readLine();
-            line2 = reader2.readLine();
-            lineNum++;
-        }
-
-        System.out.println("Files are identical");
-        return true;
-    }
 }