another round of review

broadinstitute · Oct 22, 2024 · 96cf916 · 96cf916
1 parent 4cfb521
commit 96cf916
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Showing 21 changed files with 47 additions and 47 deletions.
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java
@@ -82,7 +82,7 @@ public class FuncotatorIntegrationTest extends CommandLineProgramTest {
 
     // TODO: Get rid of this variable and use the general data sources path (issue #5350 - https://github.com/broadinstitute/gatk/issues/5350):
     private static final String DS_PIK3CA_DIR            = largeFileTestDir + "funcotator" + File.separator + "small_ds_pik3ca" + File.separator;
-    private static final String DS_PIK3CA_DIR_v43_MANE   = largeFileTestDir + "funcotator" + File.separator + "small_ds_pik3ca_v43Annotations" + File.separator;
+    private static final String DS_PIK3CA_DIR_v43_MANE   = largeFileTestDir + "funcotator" + File.separator + "ds_pik3ca_v43_WITH_MANE_SELECT_PLUS_CLINICAL_ANNOTATIONS_FOR_TEST" + File.separator;
 
     private static final String  MEDIUM_DATASOURCES_DIR     = largeFileTestDir + "funcotator" + File.separator + "funcotator_dataSources" + File.separator;
 
@@ -989,43 +989,43 @@ public void testMANESelectAnnotationDifferencesAndGencodeV43() {
         runCommandLine(arguments2);
 
         // Assert that we NEVER seen the lower priority transcript when we are in MANE select mode
-        final FeatureDataSource<VariantContext> featureDataSourceMANE = new FeatureDataSource<>(outputFileMANESelectMode);
-        final FeatureDataSource<VariantContext> featureDataSourceDefault = new FeatureDataSource<>(outputFileMANESelectMode);
-        boolean hasSeenENST00000435560 = false;
-        for (final VariantContext vc : featureDataSourceMANE) {
-            if (vc.getAttributeAsString("FUNCOTATION",null) != null) {
-                final String funcotationMANE = vc.getAttributeAsString("FUNCOTATION", "");
-                Assert.assertFalse(funcotationMANE.contains("ENST00000263967.4")); // this transcript is MANE_SELECT not MANE_PLUS_CLINICAL so should never be selected for these variants
-                Assert.assertTrue(funcotationMANE.contains("ENST00000643187.1") || funcotationMANE.contains("ENST00000435560.1"));
-                if (funcotationMANE.contains("ENST00000435560.1")) {
-                    hasSeenENST00000435560 = true;
+        try (final FeatureDataSource<VariantContext> featureDataSourceMANE = new FeatureDataSource<>(outputFileMANESelectMode);
+             final FeatureDataSource<VariantContext> featureDataSourceDefault = new FeatureDataSource<>(outputFileDefaultMode)) {
+            boolean hasSeenENST00000435560 = false;
+            for (final VariantContext vc : featureDataSourceMANE) {
+                if (vc.getAttributeAsString("FUNCOTATION", null) != null) {
+                    final String funcotationMANE = vc.getAttributeAsString("FUNCOTATION", "");
+                    Assert.assertFalse(funcotationMANE.contains("ENST00000263967.4")); // this transcript is MANE_SELECT not MANE_PLUS_CLINICAL so should never be selected for these variants
+                    Assert.assertTrue(funcotationMANE.contains("ENST00000643187.1") || funcotationMANE.contains("ENST00000435560.1"));
+                    if (funcotationMANE.contains("ENST00000435560.1")) {
+                        hasSeenENST00000435560 = true;
+                    }
                 }
             }
-        }
-        Assert.assertTrue(hasSeenENST00000435560); // ENST00000435560.1 is a basic annotation with no MANE_SELECT transcripts overlapping it, so it should still be emitted
-        hasSeenENST00000435560 = false;
-        // Assert that we see a mix of transcripts when we are in MANE select mode
-        boolean hasSeenMANESelect = false;
-        boolean hasSeenMANEPlusClinical = false;
-        for (final VariantContext vc : featureDataSourceDefault) {
-            if (vc.getAttributeAsString("FUNCOTATION", null) != null) {
-                final String funcotationDefault = vc.getAttributeAsString("FUNCOTATION", "");
-                if (funcotationDefault.contains("ENST00000643187.1")) {
-                    hasSeenMANESelect = true;
-                }
-                if (funcotationDefault.contains("ENST00000643187.1")) {
-                    hasSeenMANEPlusClinical = true;
-                }
-                if (funcotationDefault.contains("ENST00000435560.1")) {
-                    hasSeenENST00000435560 = true;
+            Assert.assertTrue(hasSeenENST00000435560); // ENST00000435560.1 is a basic annotation with no MANE_SELECT transcripts overlapping it, so it should still be emitted
+            hasSeenENST00000435560 = false;
+            // Assert that we see a mix of transcripts when we are in MANE select mode
+            boolean hasSeenMANESelect = false;
+            boolean hasSeenMANEPlusClinical = false;
+            for (final VariantContext vc : featureDataSourceDefault) {
+                if (vc.getAttributeAsString("FUNCOTATION", null) != null) {
+                    final String funcotationDefault = vc.getAttributeAsString("FUNCOTATION", "");
+                    if (funcotationDefault.contains("ENST00000643187.1")) {
+                        hasSeenMANESelect = true;
+                    }
+                    if (funcotationDefault.contains("ENST00000643187.1")) {
+                        hasSeenMANEPlusClinical = true;
+                    }
+                    if (funcotationDefault.contains("ENST00000435560.1")) {
+                        hasSeenENST00000435560 = true;
+                    }
                 }
             }
+            // assert that we have seen both versions of the transcript in the default case
+            Assert.assertTrue(hasSeenENST00000435560); // ENST00000435560.1 is a basic annotation with no MANE_SELECT transcripts overlapping it, so it should still be emitted
+            Assert.assertTrue(hasSeenMANESelect);
+            Assert.assertTrue(hasSeenMANEPlusClinical);
         }
-
-        // assert that we have seen both versions of the transcript in the default case
-        Assert.assertTrue(hasSeenENST00000435560); // ENST00000435560.1 is a basic annotation with no MANE_SELECT transcripts overlapping it, so it should still be emitted
-        Assert.assertTrue(hasSeenMANESelect);
-        Assert.assertTrue(hasSeenMANEPlusClinical);
     }
 
     //Test for https://github.com/broadinstitute/gatk/issues/6173

diff --git a/...te/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java b/...te/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java
@@ -410,16 +410,16 @@ private GencodeGtfTranscriptFeature provideArtificialTranscriptForTestMANEExtrac
 
     @DataProvider
     Object[][] provideTestForMANESelectMode() {
-        GencodeGtfTranscriptFeature NONBASIC_A = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), false, false, false);
-        GencodeGtfTranscriptFeature BASIC_A = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), true, false, false);
-        GencodeGtfTranscriptFeature BASIC_B = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 102), true, false, false);
-        GencodeGtfTranscriptFeature BASIC_MANESELECT_A = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), true, true, false);
-        GencodeGtfTranscriptFeature BASIC_MANESELECT_B = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 102), true, true, false);
-        GencodeGtfTranscriptFeature BASIC_MANEPLUSCLINICAL_A = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), true, false, true);
-        GencodeGtfTranscriptFeature BASIC_MANEPLUSCLINICAL_B = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 102), true, false, true);
-        GencodeGtfTranscriptFeature BASIC_MANESELECT_MANEPLUSCLINICAL = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), true, true, true);
-        GencodeGtfTranscriptFeature NONBASIC_MANESELECT = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), false, true, false);
-        GencodeGtfTranscriptFeature NONBASIC_MANEPLUSCLINICAL = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), false, false, true);
+        final GencodeGtfTranscriptFeature NONBASIC_A = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), false, false, false);
+        final GencodeGtfTranscriptFeature BASIC_A = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), true, false, false);
+        final GencodeGtfTranscriptFeature BASIC_B = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 102), true, false, false);
+        final GencodeGtfTranscriptFeature BASIC_MANESELECT_A = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), true, true, false);
+        final GencodeGtfTranscriptFeature BASIC_MANESELECT_B = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 102), true, true, false);
+        final GencodeGtfTranscriptFeature BASIC_MANEPLUSCLINICAL_A = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), true, false, true);
+        final GencodeGtfTranscriptFeature BASIC_MANEPLUSCLINICAL_B = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 102), true, false, true);
+        final GencodeGtfTranscriptFeature BASIC_MANESELECT_MANEPLUSCLINICAL = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), true, true, true);
+        final GencodeGtfTranscriptFeature NONBASIC_MANESELECT = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), false, true, false);
+        final GencodeGtfTranscriptFeature NONBASIC_MANEPLUSCLINICAL = provideArtificialTranscriptForTestMANEExtractMode(new SimpleInterval("chr1", 99, 101), false, false, true);
 
         return new Object[][]{
                 // trivial cases where only one transcript is present
@@ -1350,10 +1350,10 @@ Object[][] provideDataForTestCalculateGcContent() {
 
     @Test ( dataProvider = "provideTestForMANESelectMode" )
     void testMANESelectTranscriptSelectionCriteria(final List<GencodeGtfTranscriptFeature> inputTranscripts, final List<GencodeGtfTranscriptFeature> expectedTranscripts) {
-        final List<GencodeGtfTranscriptFeature> selectedTranscript = GencodeFuncotationFactory.retreiveMANESelectModeTranscriptsCriteria(inputTranscripts);
-        Assert.assertEquals(selectedTranscript.size(), expectedTranscripts.size());
-        for (GencodeGtfTranscriptFeature expectedTranscript : expectedTranscripts) {
-            Assert.assertTrue(selectedTranscript.contains(expectedTranscript));
+        final List<GencodeGtfTranscriptFeature> selectedTranscripts = GencodeFuncotationFactory.retreiveMANESelectModeTranscriptsCriteria(inputTranscripts);
+        Assert.assertEquals(selectedTranscripts.size(), expectedTranscripts.size());
+        for (int i = 0; i < selectedTranscripts.size(); i++) {
+            Assert.assertEquals(selectedTranscripts.get(i), expectedTranscripts.get(i));
         }
     }
 

diff --git a/...pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf → ...pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf b/...pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf → ...pik3ca/hg19/dummy_clinvar_hg19_pik3ca.vcf
diff --git a/...ca/hg19/dummy_clinvar_hg19_pik3ca.vcf.idx → ...ca/hg19/dummy_clinvar_hg19_pik3ca.vcf.idx b/...ca/hg19/dummy_clinvar_hg19_pik3ca.vcf.idx → ...ca/hg19/dummy_clinvar_hg19_pik3ca.vcf.idx
diff --git a/...r_pik3ca/hg19/dummy_clinvar_pik3ca.config → ...r_pik3ca/hg19/dummy_clinvar_pik3ca.config b/...r_pik3ca/hg19/dummy_clinvar_pik3ca.config → ...r_pik3ca/hg19/dummy_clinvar_pik3ca.config
diff --git a/...pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf → ...pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf b/...pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf → ...pik3ca/hg38/dummy_clinvar_hg38_pik3ca.vcf
diff --git a/...ca/hg38/dummy_clinvar_hg38_pik3ca.vcf.idx → ...ca/hg38/dummy_clinvar_hg38_pik3ca.vcf.idx b/...ca/hg38/dummy_clinvar_hg38_pik3ca.vcf.idx → ...ca/hg38/dummy_clinvar_hg38_pik3ca.vcf.idx
diff --git a/...r_pik3ca/hg38/dummy_clinvar_pik3ca.config → ...r_pik3ca/hg38/dummy_clinvar_pik3ca.config b/...r_pik3ca/hg38/dummy_clinvar_pik3ca.config → ...r_pik3ca/hg38/dummy_clinvar_pik3ca.config
diff --git a/...ations/gencode_pik3ca/hg19/gencode.config → ...R_TEST/gencode_pik3ca/hg19/gencode.config b/...ations/gencode_pik3ca/hg19/gencode.config → ...R_TEST/gencode_pik3ca/hg19/gencode.config
diff --git a/...encode_pik3ca/hg19/gencode.v19.PIK3CA.gtf → ...encode_pik3ca/hg19/gencode.v19.PIK3CA.gtf b/...encode_pik3ca/hg19/gencode.v19.PIK3CA.gtf → ...encode_pik3ca/hg19/gencode.v19.PIK3CA.gtf
diff --git a/...de_pik3ca/hg19/gencode.v19.PIK3CA.gtf.idx → ...de_pik3ca/hg19/gencode.v19.PIK3CA.gtf.idx b/...de_pik3ca/hg19/gencode.v19.PIK3CA.gtf.idx → ...de_pik3ca/hg19/gencode.v19.PIK3CA.gtf.idx
diff --git a/...a/hg19/gencode.v19.PIK3CA_transcript.dict → ...a/hg19/gencode.v19.PIK3CA_transcript.dict b/...a/hg19/gencode.v19.PIK3CA_transcript.dict → ...a/hg19/gencode.v19.PIK3CA_transcript.dict
diff --git a/.../hg19/gencode.v19.PIK3CA_transcript.fasta → .../hg19/gencode.v19.PIK3CA_transcript.fasta b/.../hg19/gencode.v19.PIK3CA_transcript.fasta → .../hg19/gencode.v19.PIK3CA_transcript.fasta
diff --git a/...9/gencode.v19.PIK3CA_transcript.fasta.fai → ...9/gencode.v19.PIK3CA_transcript.fasta.fai b/...9/gencode.v19.PIK3CA_transcript.fasta.fai → ...9/gencode.v19.PIK3CA_transcript.fasta.fai
diff --git a/...notations/gencode_pik3ca/hg38/WARNING.txt → ..._FOR_TEST/gencode_pik3ca/hg38/WARNING.txt b/...notations/gencode_pik3ca/hg38/WARNING.txt → ..._FOR_TEST/gencode_pik3ca/hg38/WARNING.txt
diff --git a/...encode_pik3ca/hg38/gencode.v43.PIK3CA.gtf → ...encode_pik3ca/hg38/gencode.v43.PIK3CA.gtf b/...encode_pik3ca/hg38/gencode.v43.PIK3CA.gtf → ...encode_pik3ca/hg38/gencode.v43.PIK3CA.gtf
diff --git a/...de_pik3ca/hg38/gencode.v43.PIK3CA.gtf.idx → ...de_pik3ca/hg38/gencode.v43.PIK3CA.gtf.idx b/...de_pik3ca/hg38/gencode.v43.PIK3CA.gtf.idx → ...de_pik3ca/hg38/gencode.v43.PIK3CA.gtf.idx
diff --git a/...a/hg38/gencode.v43.PIK3CA_transcript.dict → ...a/hg38/gencode.v43.PIK3CA_transcript.dict b/...a/hg38/gencode.v43.PIK3CA_transcript.dict → ...a/hg38/gencode.v43.PIK3CA_transcript.dict
diff --git a/.../hg38/gencode.v43.PIK3CA_transcript.fasta → .../hg38/gencode.v43.PIK3CA_transcript.fasta b/.../hg38/gencode.v43.PIK3CA_transcript.fasta → .../hg38/gencode.v43.PIK3CA_transcript.fasta
diff --git a/...8/gencode.v43.PIK3CA_transcript.fasta.fai → ...8/gencode.v43.PIK3CA_transcript.fasta.fai b/...8/gencode.v43.PIK3CA_transcript.fasta.fai → ...8/gencode.v43.PIK3CA_transcript.fasta.fai
diff --git a/...gencode_pik3ca/hg38/gencode_pik3ca.config → ...gencode_pik3ca/hg38/gencode_pik3ca.config b/...gencode_pik3ca/hg38/gencode_pik3ca.config → ...gencode_pik3ca/hg38/gencode_pik3ca.config