Adding in codec to read from Gencode GTF files. Fixes #3277

Includes tests for both hg19 and hg38.
broadinstitute · Aug 11, 2017 · b12a3ef · b12a3ef
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diff --git a/src/main/java/org/broadinstitute/hellbender/utils/codecs/GENCODE/GencodeGtfCDSFeature.java b/src/main/java/org/broadinstitute/hellbender/utils/codecs/GENCODE/GencodeGtfCDSFeature.java
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+package org.broadinstitute.hellbender.utils.codecs.GENCODE;
+
+import java.util.ArrayList;
+
+/**
+ * A Gencode GTF Feature representing a CDS.
+ *
+ * A GTF Feature represents one row of a GTF File.
+ * The specification of a GTF file is defined here:
+ * http://mblab.wustl.edu/GTF22.html
+ *
+ * Created by jonn on 7/25/17.
+ */
+// {gene,transcript,exon,CDS,UTR,start_codon,stop_codon,Selenocysteine}`
+final public class GencodeGtfCDSFeature extends GencodeGtfFeature {
+
+    private GencodeGtfCDSFeature(String[] gtfFields) {
+        super(gtfFields);
+    }
+
+    public static GencodeGtfFeature create(String[] gtfFields) {
+        return new GencodeGtfCDSFeature(gtfFields);
+    }
+
+    private GencodeGtfCDSFeature(long featureOrderNumber,
+                                 String chromosomeName,
+                                 AnnotationSource annotationSource,
+                                 FeatureType featureType,
+                                 int genomicStartLocation,
+                                 int genomicEndLocation,
+                                 GenomicStrand genomicStrand,
+                                 GenomicPhase genomicPhase,
+                                 String geneId,
+                                 String transcriptId,
+                                 GeneTranscriptType geneType,
+                                 GeneTranscriptStatus geneStatus,
+                                 String geneName,
+                                 GeneTranscriptType transcriptType,
+                                 GeneTranscriptStatus transcriptStatus,
+                                 String transcriptName,
+                                 int exonNumber,
+                                 String exonId,
+                                 LocusLevel locusLevel,
+                                 ArrayList<OptionalField<?>> optionalFields,
+                                 String anonymousOptionalFields) {
+
+        super(featureOrderNumber, chromosomeName, annotationSource, featureType, genomicStartLocation, genomicEndLocation, genomicStrand, genomicPhase, geneId, transcriptId, geneType, geneStatus, geneName, transcriptType, transcriptStatus, transcriptName, exonNumber, exonId, locusLevel, optionalFields, anonymousOptionalFields);
+    }
+
+    public static GencodeGtfFeature create(long featureOrderNumber,
+                                           String chromosomeName,
+                                           AnnotationSource annotationSource,
+                                           FeatureType featureType,
+                                           int genomicStartLocation,
+                                           int genomicEndLocation,
+                                           GenomicStrand genomicStrand,
+                                           GenomicPhase genomicPhase,
+                                           String geneId,
+                                           String transcriptId,
+                                           GeneTranscriptType geneType,
+                                           GeneTranscriptStatus geneStatus,
+                                           String geneName,
+                                           GeneTranscriptType transcriptType,
+                                           GeneTranscriptStatus transcriptStatus,
+                                           String transcriptName,
+                                           int exonNumber,
+                                           String exonId,
+                                           LocusLevel locusLevel,
+                                           ArrayList<OptionalField<?>> optionalFields,
+                                           String anonymousOptionalFields) {
+
+        return new GencodeGtfCDSFeature(featureOrderNumber, chromosomeName, annotationSource, featureType, genomicStartLocation, genomicEndLocation, genomicStrand, genomicPhase, geneId, transcriptId, geneType, geneStatus, geneName, transcriptType, transcriptStatus, transcriptName, exonNumber, exonId, locusLevel, optionalFields, anonymousOptionalFields);
+    }
+
+}