Addressed code review comments.

broadinstitute · May 29, 2018 · 3691eec · 3691eec
1 parent 87b6ce8
commit 3691eec
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Showing 3 changed files with 47 additions and 45 deletions.
diff --git a/...dinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java b/...dinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java
@@ -174,25 +174,6 @@ public class GencodeFuncotationFactory extends DataSourceFuncotationFactory {
     //==================================================================================================================
     // Constructors:
 
-    public GencodeFuncotationFactory(final Path gencodeTranscriptFastaFile, final String version) {
-        this(gencodeTranscriptFastaFile, version, DEFAULT_NAME, FuncotatorArgumentDefinitions.TRANSCRIPT_SELECTION_MODE_DEFAULT_VALUE, new HashSet<>(), new LinkedHashMap<>());
-    }
-
-    public GencodeFuncotationFactory(final Path gencodeTranscriptFastaFile, final String version, final Set<String> userRequestedTranscripts) {
-        this(gencodeTranscriptFastaFile, version, DEFAULT_NAME, FuncotatorArgumentDefinitions.TRANSCRIPT_SELECTION_MODE_DEFAULT_VALUE, userRequestedTranscripts, new LinkedHashMap<>());
-    }
-
-    public GencodeFuncotationFactory(final Path gencodeTranscriptFastaFile, final String version,final TranscriptSelectionMode transcriptSelectionMode) {
-        this(gencodeTranscriptFastaFile, version, DEFAULT_NAME, transcriptSelectionMode, new HashSet<>(), new LinkedHashMap<>());
-    }
-
-    public GencodeFuncotationFactory(final Path gencodeTranscriptFastaFile,
-                                     final String version,
-                                     final TranscriptSelectionMode transcriptSelectionMode,
-                                     final Set<String> userRequestedTranscripts) {
-        this(gencodeTranscriptFastaFile, version, DEFAULT_NAME, transcriptSelectionMode, userRequestedTranscripts, new LinkedHashMap<>());
-    }
-
     public GencodeFuncotationFactory(final Path gencodeTranscriptFastaFile,
                                      final String version,
                                      final String name,

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java
@@ -203,24 +203,24 @@ public Object[][] provideForLargeDataValidationTest() {
                         true,
                         FuncotatorTestConstants.REFERENCE_VERSION_HG19,
                 },
-//                {
-//                        "C828.TCGA-D3-A2JP-06A-11D-A19A-08.3-filtered.PASS.vcf",
-//                        "Homo_sapiens_assembly19.fasta",
-//                        true,
-//                        FuncotatorTestConstants.REFERENCE_VERSION_HG19
-//                },
-//                {
-//                        "hg38_test_variants.vcf",
-//                        "Homo_sapiens_assembly38.fasta",
-//                        false,
-//                        FuncotatorTestConstants.REFERENCE_VERSION_HG38
-//                },
-//                {
-//                        "sample21.trimmed.vcf",
-//                        "Homo_sapiens_assembly38.fasta",
-//                        false,
-//                        FuncotatorTestConstants.REFERENCE_VERSION_HG38
-//                }
+                {
+                        "C828.TCGA-D3-A2JP-06A-11D-A19A-08.3-filtered.PASS.vcf",
+                        "Homo_sapiens_assembly19.fasta",
+                        true,
+                        FuncotatorTestConstants.REFERENCE_VERSION_HG19
+                },
+                {
+                        "hg38_test_variants.vcf",
+                        "Homo_sapiens_assembly38.fasta",
+                        false,
+                        FuncotatorTestConstants.REFERENCE_VERSION_HG38
+                },
+                {
+                        "sample21.trimmed.vcf",
+                        "Homo_sapiens_assembly38.fasta",
+                        false,
+                        FuncotatorTestConstants.REFERENCE_VERSION_HG38
+                }
         };
     }
 

diff --git a/...te/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java b/...te/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java
@@ -16,10 +16,7 @@
 import org.broadinstitute.hellbender.engine.ReferenceDataSource;
 import org.broadinstitute.hellbender.engine.ReferenceMemorySource;
 import org.broadinstitute.hellbender.exceptions.GATKException;
-import org.broadinstitute.hellbender.tools.funcotator.Funcotation;
-import org.broadinstitute.hellbender.tools.funcotator.FuncotatorTestConstants;
-import org.broadinstitute.hellbender.tools.funcotator.SequenceComparison;
-import org.broadinstitute.hellbender.tools.funcotator.TranscriptSelectionMode;
+import org.broadinstitute.hellbender.tools.funcotator.*;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.codecs.gencode.*;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
@@ -65,7 +62,13 @@ public class GencodeFuncotationFactoryUnitTest extends GATKBaseTest {
 
         // Gets cleaned up in `cleanupAfterTests()`
         // NOTE: This is initialized here to save time in testing.
-        testMuc16SnpCreateFuncotationsFuncotationFactory = new GencodeFuncotationFactory(IOUtils.getPath(FuncotatorTestConstants.MUC16_GENCODE_TRANSCRIPT_FASTA_FILE), "VERSION");
+        testMuc16SnpCreateFuncotationsFuncotationFactory = new GencodeFuncotationFactory(
+                IOUtils.getPath(FuncotatorTestConstants.MUC16_GENCODE_TRANSCRIPT_FASTA_FILE),
+                "VERSION",
+                GencodeFuncotationFactory.DEFAULT_NAME,
+                FuncotatorArgumentDefinitions.TRANSCRIPT_SELECTION_MODE_DEFAULT_VALUE,
+                new HashSet<>(),
+                new LinkedHashMap<>());
     }
 
     //==================================================================================================================
@@ -1147,7 +1150,13 @@ void testMuc16SnpCreateFuncotations(final int chromosomeNumber,
         final Set<String> requestedTranscriptIds = getValidTranscriptsForGene("MUC16");
 
         // Create a factory for our funcotations:
-        try (final GencodeFuncotationFactory funcotationFactory = new GencodeFuncotationFactory(new File(FuncotatorTestConstants.MUC16_GENCODE_TRANSCRIPT_FASTA_FILE).toPath(), "VERSION", requestedTranscriptIds)) {
+        try (final GencodeFuncotationFactory funcotationFactory = new GencodeFuncotationFactory(
+                IOUtils.getPath(FuncotatorTestConstants.MUC16_GENCODE_TRANSCRIPT_FASTA_FILE),
+                "VERSION",
+                GencodeFuncotationFactory.DEFAULT_NAME,
+                FuncotatorArgumentDefinitions.TRANSCRIPT_SELECTION_MODE_DEFAULT_VALUE,
+                requestedTranscriptIds,
+                new LinkedHashMap<>())) {
 
             // Generate our funcotations:
             final List<Feature> featureList = new ArrayList<>();
@@ -1198,7 +1207,13 @@ void createNonBasicFuncotations(final int start, final int end) {
         final ReferenceContext referenceContext = new ReferenceContext(refDataSourceHg19Ch19, variantInterval );
 
         // Create a factory for our funcotations:
-        try (final GencodeFuncotationFactory funcotationFactory = new GencodeFuncotationFactory(new File(FuncotatorTestConstants.MUC16_GENCODE_TRANSCRIPT_FASTA_FILE).toPath(), "VERSION")) {
+        try (final GencodeFuncotationFactory funcotationFactory = new GencodeFuncotationFactory(
+                                                                    IOUtils.getPath(FuncotatorTestConstants.MUC16_GENCODE_TRANSCRIPT_FASTA_FILE),
+                                                                    "VERSION",
+                                                                    GencodeFuncotationFactory.DEFAULT_NAME,
+                                                                    FuncotatorArgumentDefinitions.TRANSCRIPT_SELECTION_MODE_DEFAULT_VALUE,
+                                                                    new HashSet<>(),
+                                                                    new LinkedHashMap<>())) {
 
             // Generate our funcotations:
             final List<Feature> featureList = new ArrayList<>();
@@ -1262,7 +1277,13 @@ void testCreateFuncotations(final String expectedGeneName,
         final Set<String> requestedTranscriptIds = getValidTranscriptsForGene(expectedGeneName);
 
         // Create a factory for our funcotations:
-        try (final GencodeFuncotationFactory funcotationFactory = new GencodeFuncotationFactory(IOUtils.getPath(transcriptFastaFile), "VERSION", requestedTranscriptIds)) {
+        try (final GencodeFuncotationFactory funcotationFactory = new GencodeFuncotationFactory(
+                IOUtils.getPath(transcriptFastaFile),
+                "VERSION",
+                GencodeFuncotationFactory.DEFAULT_NAME,
+                FuncotatorArgumentDefinitions.TRANSCRIPT_SELECTION_MODE_DEFAULT_VALUE,
+                requestedTranscriptIds,
+                new LinkedHashMap<>())) {
 
             final List<Feature> featureList = new ArrayList<>();
             featureList.add( gene );