fix: remove set functions in GtfInfo

broadinstitute · Aug 9, 2024 · 865ffd4 · 865ffd4
1 parent df07f5b
commit 865ffd4
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Showing 3 changed files with 28 additions and 36 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfInfo.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfInfo.java
@@ -9,9 +9,9 @@ public enum Type{
         TRANSCRIPT
     }
 
-    private Type type;
+    private final Type type;
     private final String geneName;
-    private Interval interval;
+    private final Interval interval;
 
     public GtfInfo(Interval interval, Type type, String geneName) {
         this.interval = interval;
@@ -23,10 +23,6 @@ public Type getType() {
         return type;
     }
 
-    public void setType(Type type) {
-        this.type = type;
-    }
-
     public String getGeneName() {
         return geneName;
     }
@@ -43,10 +39,6 @@ public Integer getEnd() {
         return interval.getEnd();
     }
 
-    public void setInterval(Interval interval) {
-        this.interval = interval;
-    }
-
     @Override
     public String toString() {
         return "GtfInfo{ " + "type = " + type + " geneName = " + geneName + "interval = " + interval;

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
@@ -97,7 +97,8 @@ public class GtfToBed extends FeatureWalker<GencodeGtfFeature> {
     @Argument( fullName = SORT_BY_BASIC_LONG_NAME, doc = "Only use basic transcripts")
     public boolean sortByBasic = false;
 
-    private final Map<String, GtfInfo> idToInfo = new HashMap<>();
+    //stores either gene or transcript ID and summary information about the feature
+    private final Map<String, GtfInfo> featureInfoMap = new HashMap<>();
 
     @Override
     protected boolean isAcceptableFeatureType(Class<? extends Feature> featureType) {
@@ -160,7 +161,7 @@ private void processGeneFeature(GencodeGtfFeature gtfFeature) {
         final GtfInfo gtfInfo = new GtfInfo(interval, GtfInfo.Type.GENE, gtfFeature.getGeneName());
 
         // store in hashmap with key as geneId
-        idToInfo.put(gtfFeature.getGeneId(), gtfInfo);
+        featureInfoMap.put(gtfFeature.getGeneId(), gtfInfo);
     }
 
     // stores the transcript ID and Interval info in hashmap
@@ -170,7 +171,7 @@ private void processTranscriptFeature(GencodeGtfFeature gtfFeature) {
         final GtfInfo gtfInfo = new GtfInfo(interval, GtfInfo.Type.TRANSCRIPT, gtfFeature.getGeneName());
 
         //store in hashmap with key as transcriptId
-        idToInfo.put(gtfFeature.getTranscriptId(), gtfInfo);
+        featureInfoMap.put(gtfFeature.getTranscriptId(), gtfInfo);
 
         //update start/end of corresponding gene if needed
         updateGeneStart(gtfFeature);
@@ -180,34 +181,34 @@ private void processTranscriptFeature(GencodeGtfFeature gtfFeature) {
     // update the gene interval start position based on the transcript
     private void updateGeneStart(GencodeGtfFeature gtfFeature) {
         // get the start value of the gene
-        int geneStart = idToInfo.get(gtfFeature.getGeneId()).getStart();
+        int geneStart = featureInfoMap.get(gtfFeature.getGeneId()).getStart();
 
         // if the transcript start is less than the gene start
         if (gtfFeature.getStart() < geneStart) {
             // set the gene start to be the transcript start
             geneStart = gtfFeature.getStart();
-            updateGeneInterval(gtfFeature, geneStart, idToInfo.get(gtfFeature.getGeneId()).getEnd());
+            updateGeneInterval(gtfFeature, geneStart, featureInfoMap.get(gtfFeature.getGeneId()).getEnd());
         }
     }
 
     // update the gene interval end position based on the transcript
     private void updateGeneEnd(GencodeGtfFeature gtfFeature) {
         // get the end value of the gene
-        int geneEnd = idToInfo.get(gtfFeature.getGeneId()).getEnd();
+        int geneEnd = featureInfoMap.get(gtfFeature.getGeneId()).getEnd();
 
         // if the transcript start is greater than the gene start
         if (gtfFeature.getEnd() > geneEnd) {
             // set the gene end to be the transcript end
             geneEnd = gtfFeature.getEnd();
-            updateGeneInterval(gtfFeature, idToInfo.get(gtfFeature.getGeneId()).getStart(), geneEnd);
+            updateGeneInterval(gtfFeature, featureInfoMap.get(gtfFeature.getGeneId()).getStart(), geneEnd);
         }
     }
 
     // updates an interval of the gene if it needs to be changed
     private void updateGeneInterval(GencodeGtfFeature gtfFeature, int geneStart, int geneEnd) {
         Interval geneInterval = new Interval(gtfFeature.getContig(), geneStart, geneEnd);
         GtfInfo gtfGeneInfo = new GtfInfo(geneInterval, GtfInfo.Type.GENE, gtfFeature.getGeneName());
-        idToInfo.put(gtfFeature.getGeneId(), gtfGeneInfo);
+        featureInfoMap.put(gtfFeature.getGeneId(), gtfGeneInfo);
     }
 
     // runs immediately after it has gone through each line of gtf (apply method)
@@ -245,8 +246,8 @@ public static class GtfInfoComparator implements Comparator<Map.Entry<String, Gt
         // compare two entries of a map where key = geneId or transcriptId and value = gtfInfo object
         @Override
         public int compare(Map.Entry<String, GtfInfo> e1, Map.Entry<String, GtfInfo> e2) {
-            Interval e1Interval = e1.getValue().getInterval();
-            Interval e2Interval = e2.getValue().getInterval();
+            final Interval e1Interval = e1.getValue().getInterval();
+            final Interval e2Interval = e2.getValue().getInterval();
 
             Utils.nonNull(dictionary.getSequence(e1Interval.getContig()), "could not get sequence for " + e1Interval.getContig());
             Utils.nonNull(dictionary.getSequence(e2Interval.getContig()), "could not get sequence for " + e2Interval.getContig());
@@ -275,7 +276,7 @@ public int compare(Map.Entry<String, GtfInfo> e1, Map.Entry<String, GtfInfo> e2)
     // sorts the map containing the features based on contig and start position
     private LinkedHashMap<String, GtfInfo> getSortedMap(SAMSequenceDictionary sequenceDictionary) {
         // create a list that has the keys and values of idToInfo and sort the list using GtfInfoComparator
-        List<Map.Entry<String, GtfInfo>> entries = new ArrayList<>(idToInfo.entrySet());
+        List<Map.Entry<String, GtfInfo>> entries = new ArrayList<>(featureInfoMap.entrySet());
         entries.sort(new GtfInfoComparator(sequenceDictionary));
 
         // put each (sorted) entry in the list into a linked hashmap

diff --git a/.../java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBedIntegrationTest.java b/.../java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBedIntegrationTest.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.hellbender.tools.walkers.conversion;
 
 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;
@@ -18,13 +17,13 @@ public class GtfToBedIntegrationTest extends CommandLineProgramTest {
     private static final File mouse = new File(ConversionTestUtils.getMouseGtf());
     private static final File mouseDictionary = new File(ConversionTestUtils.getMouseDict());
     private static final File dictionary = new File(ConversionTestUtils.getReferenceDict());
-    private static final File decoysGeneBed = new File(ConversionTestUtils.getDecoySamplesGeneBed());
-    private static final File decoysTranscriptBed = new File(ConversionTestUtils.getDecoySamplesTranscriptBed());
-    private static final File mapk1GeneBed = new File(ConversionTestUtils.getMapk1GeneBed());
-    private static final File mapk1TranscriptBed = new File(ConversionTestUtils.getMapk1TranscriptBed());
-    private static final File manyTranscriptsBed = new File (ConversionTestUtils.getManyTranscriptsBed());
-    private static final File notBasicBed = new File(ConversionTestUtils.getNotBasicBed());
-    private static final File mouseBed = new File(ConversionTestUtils.getMouseBed());
+    private static final File expectedDecoysGeneBed = new File(ConversionTestUtils.getDecoySamplesGeneBed());
+    private static final File expectedDecoysTranscriptBed = new File(ConversionTestUtils.getDecoySamplesTranscriptBed());
+    private static final File expectedMapk1GeneBed = new File(ConversionTestUtils.getMapk1GeneBed());
+    private static final File expectedMapk1TranscriptBed = new File(ConversionTestUtils.getMapk1TranscriptBed());
+    private static final File expectedManyTranscriptsBed = new File (ConversionTestUtils.getManyTranscriptsBed());
+    private static final File expectedNotBasicBed = new File(ConversionTestUtils.getNotBasicBed());
+    private static final File expectedMouseBed = new File(ConversionTestUtils.getMouseBed());
 
     // tests specifically mapk1 gene
     @Test
@@ -77,10 +76,10 @@ private void runMapk1(boolean transcript) throws IOException {
 
         if (transcript) {
             Assert.assertEquals(countLines(outputFile), 3);
-            IntegrationTestSpec.assertEqualTextFiles(mapk1TranscriptBed, outputFile);
+            IntegrationTestSpec.assertEqualTextFiles(expectedMapk1TranscriptBed, outputFile);
         } else {
             Assert.assertEquals(countLines(outputFile), 1);
-            IntegrationTestSpec.assertEqualTextFiles(mapk1GeneBed, outputFile);
+            IntegrationTestSpec.assertEqualTextFiles(expectedMapk1GeneBed, outputFile);
         }
     }
 
@@ -96,11 +95,11 @@ private void runDecoySample(boolean transcript) throws IOException {
 
         if (transcript) {
             Assert.assertEquals(countLines(outputFile), 20);
-            IntegrationTestSpec.assertEqualTextFiles(decoysTranscriptBed, outputFile);
+            IntegrationTestSpec.assertEqualTextFiles(expectedDecoysTranscriptBed, outputFile);
 
         } else {
             Assert.assertEquals(countLines(outputFile), 19);
-            IntegrationTestSpec.assertEqualTextFiles(decoysGeneBed, outputFile);
+            IntegrationTestSpec.assertEqualTextFiles(expectedDecoysGeneBed, outputFile);
         }
     }
 
@@ -112,7 +111,7 @@ private void runManyTranscripts() throws IOException {
                 .add(GtfToBed.SORT_BY_BASIC_LONG_NAME, true)
                 .addOutput(outputFile);
         runCommandLine(argsBuilder);
-        IntegrationTestSpec.assertEqualTextFiles(manyTranscriptsBed, outputFile);
+        IntegrationTestSpec.assertEqualTextFiles(expectedManyTranscriptsBed, outputFile);
 
     }
 
@@ -124,7 +123,7 @@ private void runNotBasic() throws IOException {
                 .add(GtfToBed.SORT_BY_BASIC_LONG_NAME, false)
                 .addOutput(outputFile);
         runCommandLine(argsBuilder);
-        IntegrationTestSpec.assertEqualTextFiles(notBasicBed, outputFile);
+        IntegrationTestSpec.assertEqualTextFiles(expectedNotBasicBed, outputFile);
     }
 
     private void runMouse() throws IOException {
@@ -135,7 +134,7 @@ private void runMouse() throws IOException {
                 .add(GtfToBed.SORT_BY_BASIC_LONG_NAME, false)
                 .addOutput(outputFile);
         runCommandLine(argsBuilder);
-        IntegrationTestSpec.assertEqualTextFiles(mouseBed, outputFile);
+        IntegrationTestSpec.assertEqualTextFiles(expectedMouseBed, outputFile);
     }
 
     private int countLines(File file) throws IOException {