diff --git a/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGTFFieldConstants.java b/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGTFFieldConstants.java index 151835f9305..0bea193cb3c 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGTFFieldConstants.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGTFFieldConstants.java @@ -12,6 +12,48 @@ * be instantiated if necessary to preserve the spec compliance of funcotator against future releases of Gencode. */ public class GencodeGTFFieldConstants { + + /** + * A list of required fields from the GencodeGTF codec. These are the fields that are currently first-class members of the + * GencodeGTFFeature and are handled specially handled by the GencodeGTFCodec. + */ + public static final String GENE_ID = "gene_id"; + public static final String TRANSCRIPT_ID = "transcript_id"; + public static final String GENE_TYPE = "gene_type"; + public static final String GENE_BIOTYPE = "gene_biotype"; + public static final String GENE_STATUS = "gene_status"; + public static final String GENE_NAME = "gene_name"; + public static final String TRANSCRIPT_TYPE = "transcript_type"; + public static final String TRANSCRIPT_BIOTYPE = "transcript_biotype"; + public static final String TRANSCRIPT_STATUS = "transcript_status"; + public static final String TRANSCRIPT_NAME = "transcript_name"; + public static final String LEVEL = "level"; + + // Mandatory except in Gene and Transcript lines (not enforced by this codec) + public static final String EXON_NUMBER = "exon_number"; + public static final String EXON_ID = "exon_id"; + + public class GencodeOptionalFields { + /** + * Spec optional gencode fields: + */ + public static final String TAG = "tag"; + public static final String CCDSID = "ccdsid"; + public static final String HAVANA_GENE = "havana_gene"; + public static final String HAVANA_TRANSCRIPT = "havana_transcript"; + public static final String PROTEIN_ID = "protein_id"; + public static final String ONT = "ont"; + public static final String TRANSCRIPT_SUPPORT_LEVEL = "transcript_support_level"; + public static final String REMAP_STATUS = "remap_status"; + public static final String REMAP_ORIGINAL_ID = "remap_original_id"; + public static final String REMAP_ORIGINAL_LOCATION = "remap_original_location"; + public static final String REMAP_NUM_MAPPINGS = "remap_num_mappings"; + public static final String REMAP_TARGET_STATUS = "remap_target_status"; + public static final String REMAP_SUBSTITUTED_MISSING_TARGET = "remap_substituted_missing_target"; + public static final String HGNC_ID = "hgnc_id"; + public static final String MGI_ID = "mgi_id"; + } + /** * Biotype / transcript type for the transcript or gene represented in a feature. * This is a tag of some biological function associated with a feature. diff --git a/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodec.java b/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodec.java index 7181a4c1daa..f7bf48e0329 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodec.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodec.java @@ -69,7 +69,7 @@ final public class GencodeGtfCodec extends AbstractGtfCodec { /** * Maximum version of gencode that will not generate a warning. This parser will still attempt to parse versions above this number, but a warning about potential errors will appear. */ - private static final int GENCODE_GTF_MAX_VERSION_NUM_INCLUSIVE = 43; + private static final int GENCODE_GTF_MAX_TESTED_VERSION = 43; private int currentLineNum = 1; private final List header = new ArrayList<>(); @@ -315,8 +315,8 @@ boolean validateHeader(final List header, final boolean throwIfInvalid) } } - if (versionNumber > GENCODE_GTF_MAX_VERSION_NUM_INCLUSIVE) { - logger.warn("GENCODE GTF Header line 1 has a version number that is above maximum tested version (v " + GENCODE_GTF_MAX_VERSION_NUM_INCLUSIVE + ") (given: " + + if (versionNumber > GENCODE_GTF_MAX_TESTED_VERSION) { + logger.warn("GENCODE GTF Header line 1 has a version number that is above maximum tested version (v " + GENCODE_GTF_MAX_TESTED_VERSION + ") (given: " + versionNumber + "): " + header.get(0) + " Continuing, but errors may occur."); } } diff --git a/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfFeature.java b/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfFeature.java index 643b5213c61..d89a8af7e73 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfFeature.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfFeature.java @@ -148,38 +148,38 @@ protected GencodeGtfFeature(final String[] gtfFields, final String gtfFileType) switch (fieldName) { // Find the right field to set: - case "gene_id": + case GencodeGTFFieldConstants.GENE_ID: baseData.geneId = fieldValue; break; - case "transcript_id": + case GencodeGTFFieldConstants.TRANSCRIPT_ID: baseData.transcriptId = fieldValue; break; - case "gene_type": + case GencodeGTFFieldConstants.GENE_TYPE: baseData.geneType = fieldValue; break; // For ENSEMBL GTF files: - case "gene_biotype": + case GencodeGTFFieldConstants.GENE_BIOTYPE: baseData.geneType = fieldValue; break; - case "gene_status": + case GencodeGTFFieldConstants.GENE_STATUS: baseData.geneStatus = fieldValue; break; - case "gene_name": + case GencodeGTFFieldConstants.GENE_NAME: baseData.geneName = fieldValue; break; - case "transcript_type": + case GencodeGTFFieldConstants.TRANSCRIPT_TYPE: baseData.transcriptType = fieldValue; break; - case "transcript_biotype": + case GencodeGTFFieldConstants.TRANSCRIPT_BIOTYPE: baseData.transcriptType = fieldValue; break; - case "transcript_status": + case GencodeGTFFieldConstants.TRANSCRIPT_STATUS: baseData.transcriptStatus = fieldValue; break; - case "transcript_name": + case GencodeGTFFieldConstants.TRANSCRIPT_NAME: baseData.transcriptName = fieldValue; break; - case "exon_number": + case GencodeGTFFieldConstants.EXON_NUMBER: try { baseData.exonNumber = Integer.valueOf(fieldValue); } @@ -187,61 +187,14 @@ protected GencodeGtfFeature(final String[] gtfFields, final String gtfFileType) throw new UserException.MalformedFile("Could not convert field value into integer: " + fieldValue); } break; - case "exon_id": + case GencodeGTFFieldConstants.EXON_ID: baseData.exonId = fieldValue; break; - case "level": + case GencodeGTFFieldConstants.LEVEL: baseData.locusLevel = fieldValue; break; - case "tag": - optionalField = new OptionalField<>(fieldName, fieldValue); - break; - case "ccdsid": - optionalField = new OptionalField<>(fieldName, fieldValue); - break; - case "havana_gene": - optionalField = new OptionalField<>(fieldName, fieldValue); - break; - case "havana_transcript": - optionalField = new OptionalField<>(fieldName, fieldValue); - break; - case "protein_id": - optionalField = new OptionalField<>(fieldName, fieldValue); - break; - case "ont": - optionalField = new OptionalField<>(fieldName, fieldValue); - break; - case "transcript_support_level": - optionalField = new OptionalField<>(fieldName, fieldValue); - break; - case "remap_status": - optionalField = new OptionalField<>(fieldName, fieldValue); - break; - case "remap_original_id": - optionalField = new OptionalField<>(fieldName, fieldValue); - break; - case "remap_original_location": - try { - optionalField = new OptionalField<>(fieldName, Long.valueOf(fieldValue)); - } - catch (final NumberFormatException nfe) { - // We must have gotten a field that has a different format. - // For now, just copy it over: - optionalField = new OptionalField<>(fieldName, fieldValue); - } - break; - case "remap_num_mappings": - optionalField = new OptionalField<>(fieldName, Long.valueOf(fieldValue)); - break; - case "remap_target_status": - optionalField = new OptionalField<>(fieldName, fieldValue); - break; - case "remap_substituted_missing_target": - optionalField = new OptionalField<>(fieldName, fieldValue); - break; default: - anonymousOptionalFieldBuilder.append(extraField); - anonymousOptionalFieldBuilder.append(EXTRA_FIELD_DELIMITER); + optionalField = new OptionalField<>(fieldName, fieldValue); break; } @@ -250,11 +203,6 @@ protected GencodeGtfFeature(final String[] gtfFields, final String gtfFileType) baseData.optionalFields.add(optionalField); } } - - // Save our anonymous optional fields: - if ( anonymousOptionalFieldBuilder.length() != 0 ) { - baseData.anonymousOptionalFields = anonymousOptionalFieldBuilder.toString(); - } } /** @@ -458,10 +406,6 @@ private String serializeToStringHelper() { baseData.optionalFields.stream().map(Object::toString).collect(Collectors.joining(" ")) ); - if ( baseData.anonymousOptionalFields != null ) { - stringBuilder.append(baseData.anonymousOptionalFields); - } - return stringBuilder.toString().trim(); } @@ -581,11 +525,7 @@ public List> getOptionalFields() { return baseData.optionalFields; } - public String getAnonymousOptionalFields() { - return baseData.anonymousOptionalFields; - } - - // Certian optional fields support multiple values, so we need to return a list of them. + // Certian optional fields support multiple values (for example "tag"), so we need to return a list of them. public List> getOptionalField(final String key) { final List> optionalFields = new ArrayList<>(); for (final OptionalField optionalField : baseData.optionalFields) { diff --git a/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfFeatureBaseData.java b/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfFeatureBaseData.java index 47863f74dca..e998feede3c 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfFeatureBaseData.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfFeatureBaseData.java @@ -83,17 +83,13 @@ final public class GencodeGtfFeatureBaseData { /** * Optional GENCODE GTF Fields. + * This also includes unidentified GTF fields that may not be specified in the Gencode GTF specification. * For details, see the following: * https://www.gencodegenes.org/data_format.html * https://www.gencodegenes.org/gencode_tags.html */ public List> optionalFields = new ArrayList<>(); - /** - * Additional optional GTF fields. - */ - public String anonymousOptionalFields = null; - public GencodeGtfFeatureBaseData() {} public GencodeGtfFeatureBaseData( @@ -117,8 +113,7 @@ public GencodeGtfFeatureBaseData( final int exonNumber, final String exonId, final String locusLevel, - final List> optionalFields, - final String anonymousOptionalFields + final List> optionalFields ) { this.gtfSourceFileType = gtfSourceFileType; this.featureOrderNumber = featureOrderNumber; @@ -145,7 +140,6 @@ public GencodeGtfFeatureBaseData( this.optionalFields = optionalFields; } - this.anonymousOptionalFields = anonymousOptionalFields; } @Override @@ -183,8 +177,7 @@ else if ( this == that ) { Objects.equals(exonNumber, thatBaseData.exonNumber) && Objects.equals(exonId, thatBaseData.exonId) && Objects.equals(locusLevel, thatBaseData.locusLevel) && - Objects.equals(anonymousOptionalFields, thatBaseData.anonymousOptionalFields) && - Objects.equals(optionalFields, thatBaseData.optionalFields); + Objects.equals(optionalFields, thatBaseData.optionalFields); //TODO should equality enforce the order of the optional fields? } return isEqual; @@ -211,7 +204,6 @@ public int hashCode() { result = 31 * result + (exonId != null ? exonId.hashCode() : 0); result = 31 * result + (locusLevel != null ? locusLevel.hashCode() : 0); result = 31 * result + (optionalFields != null ? optionalFields.hashCode() : 0); - result = 31 * result + (anonymousOptionalFields != null ? anonymousOptionalFields.hashCode() : 0); return result; } } diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/DataProviderForExampleGencodeGtfGene.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/DataProviderForExampleGencodeGtfGene.java index 3353ef3da7f..0e020b927e5 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/DataProviderForExampleGencodeGtfGene.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/DataProviderForExampleGencodeGtfGene.java @@ -24,7 +24,7 @@ public static GencodeGtfGeneFeature createGencodeGtfGeneFeature() { data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 1, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.GENE, 1, 3000, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", null, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), - null, "TEST_GENE", null, null, null, -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), null, null); + null, "TEST_GENE", null, null, null, -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), null); final GencodeGtfGeneFeature gene = (GencodeGtfGeneFeature)GencodeGtfFeature.create(data); // ====================== @@ -32,72 +32,63 @@ public static GencodeGtfGeneFeature createGencodeGtfGeneFeature() { data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 2, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.TRANSCRIPT, 1, 1000, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfTranscriptFeature transcript1 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 3, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 1, 200, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 1, "TEST_EXON1", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon1 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 4, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.START_CODON, 99, 101, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 1, "TEST_EXON1", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfStartCodonFeature startCodon1 = (GencodeGtfStartCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 5, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 201, 400, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 2, "TEST_EXON2", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon2 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 6, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 201, 400, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 2, "TEST_EXON2", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfCDSFeature cds1 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 7, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 401, 600, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 3, "TEST_EXON3", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon3 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 8, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 401, 600, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 3, "TEST_EXON3", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfCDSFeature cds2 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 9, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 601, 800, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 4, "TEST_EXON4", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon4 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 10, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 601, 800, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 4, "TEST_EXON4", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfCDSFeature cds3 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); @@ -105,32 +96,28 @@ public static GencodeGtfGeneFeature createGencodeGtfGeneFeature() { data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 11, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 801, 1000, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 5, "TEST_EXON5", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon5 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 12, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.STOP_CODON, 900, 902, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 5, "TEST_EXON5", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfStopCodonFeature stopCodon1 = (GencodeGtfStopCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 13, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, 1, 98, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 1, "TEST_EXON1", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfUTRFeature utr1 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 14, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, 903, 1000, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 5, "TEST_EXON5", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfUTRFeature utr2 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); @@ -139,80 +126,70 @@ public static GencodeGtfGeneFeature createGencodeGtfGeneFeature() { data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 15, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.TRANSCRIPT, 1001, 2000, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfTranscriptFeature transcript2 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 16, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 1001, 1200, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 1, "TEST_EXON1", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon6 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 17, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.START_CODON, 1099, 1101, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 1, "TEST_EXON1", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfStartCodonFeature startCodon2 = (GencodeGtfStartCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 18, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 1099, 1200, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 1, "TEST_EXON1", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfCDSFeature cds4 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 19, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 1201, 1400, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 2, "TEST_EXON2", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon7 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 20, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 1201, 1400, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 2, "TEST_EXON2", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfCDSFeature cds5 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 21, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 1401, 1600, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 3, "TEST_EXON3", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon8 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 22, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 1401, 1600, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 3, "TEST_EXON3", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfCDSFeature cds6 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 23, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 1601, 1800, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 4, "TEST_EXON4", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon9 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 24, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 1601, 1800, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 4, "TEST_EXON4", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfCDSFeature cds7 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); @@ -220,40 +197,35 @@ public static GencodeGtfGeneFeature createGencodeGtfGeneFeature() { data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 25, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 1801, 2000, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 5, "TEST_EXON5", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon10 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 26, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 1801, 1899, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 5, "TEST_EXON5", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfCDSFeature cds8 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 27, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.STOP_CODON, 1900, 1902, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 5, "TEST_EXON5", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfStopCodonFeature stopCodon2 = (GencodeGtfStopCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 28, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, 1001, 1098, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 1, "TEST_EXON1", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfUTRFeature utr3 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 29, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, 1903, 2000, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT2", 5, "TEST_EXON5", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfUTRFeature utr4 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); @@ -262,48 +234,42 @@ public static GencodeGtfGeneFeature createGencodeGtfGeneFeature() { data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 30, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.TRANSCRIPT, 2001, 3000, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT3", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT3", -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfTranscriptFeature transcript3 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 31, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 2001, 2200, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT3", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT3", 1, "TEST_EXON1", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon11 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 32, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 2201, 2400, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT3", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT3", 2, "TEST_EXON2", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon12 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 33, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 2401, 2600, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT3", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT3", 3, "TEST_EXON3", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon13 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 34, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 2601, 2800, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT3", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT3", 4, "TEST_EXON4", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon14 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 35, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 2801, 3000, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT3", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT3", 5, "TEST_EXON5", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon15 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); @@ -454,14 +420,13 @@ public static GencodeGtfGeneFeature dynamicallyCreateTestGencodeGtfGeneFeature(f final GencodeGtfFeatureBaseData tmpGene = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.GENE, start, start + totalLength - 1, codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", null, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), - null, geneName, null, null, null, -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), null, null); + null, geneName, null, null, null, -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), null); final GencodeGtfGeneFeature gene = (GencodeGtfGeneFeature)GencodeGtfFeature.create(tmpGene); final GencodeGtfFeatureBaseData tmpTranscript = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.TRANSCRIPT, gene.getGenomicStartLocation(), gene.getGenomicEndLocation(), codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfTranscriptFeature transcript1 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(tmpTranscript); @@ -531,8 +496,7 @@ private static GencodeGtfExonFeature createStopCodonExon(final int exonStart, fi final GencodeGtfFeatureBaseData data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, exonStart, exonStart + lengthExons + length3pUtr - 1, codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", exonNum, "TEST_EXON_" + exonNum, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); @@ -542,8 +506,7 @@ private static GencodeGtfExonFeature createStopCodonExon(final int exonStart, fi final GencodeGtfFeatureBaseData tmpCdsMinusStop = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, cdsStart, cdsEnd, codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", exon.getExonNumber(), exon.getExonId(), GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfCDSFeature cds1 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(tmpCdsMinusStop); @@ -553,8 +516,7 @@ private static GencodeGtfExonFeature createStopCodonExon(final int exonStart, fi final GencodeGtfFeatureBaseData tmpStopCodon = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.STOP_CODON, stopCodonStart, stopCodonEnd, codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", exon.getExonNumber(), exon.getExonId(), GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfStopCodonFeature stopCodon1 = (GencodeGtfStopCodonFeature) GencodeGtfFeature.create(tmpStopCodon); @@ -572,8 +534,7 @@ private static GencodeGtfUTRFeature create3pUtr(final AtomicInteger featureOrder final GencodeGtfFeatureBaseData tmp3pUtr = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, start, end, codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", exon.getExonNumber(), exon.getExonId(), GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); return (GencodeGtfUTRFeature) GencodeGtfFeature.create(tmp3pUtr); } @@ -587,8 +548,7 @@ private static GencodeGtfUTRFeature create5pUtr(final AtomicInteger featureOrder final GencodeGtfFeatureBaseData tmp5pUtr = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, start, end, codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", exon.getExonNumber(), exon.getExonId(), GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); return (GencodeGtfUTRFeature) GencodeGtfFeature.create(tmp5pUtr); } @@ -601,8 +561,7 @@ private static GencodeGtfExonFeature createStartCodonExon(final int exonStart, f final GencodeGtfFeatureBaseData tmpExon = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, exonStart, exonStart + length5pUtr + lengthExons - 1, codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", exonNum, "TEST_EXON_" + exonNum, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon = (GencodeGtfExonFeature) GencodeGtfFeature.create(tmpExon); @@ -610,16 +569,14 @@ private static GencodeGtfExonFeature createStartCodonExon(final int exonStart, f final GencodeGtfFeatureBaseData tmpStartCodon = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.START_CODON, exon.getGenomicStartLocation() + length5pUtr - 1, exon.getGenomicStartLocation() + length5pUtr + 1, codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 1, "TEST_EXON1", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfStartCodonFeature startCodon1 = (GencodeGtfStartCodonFeature) GencodeGtfFeature.create(tmpStartCodon); final GencodeGtfFeatureBaseData tmpCdsMinusStart = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, startCodon1.getGenomicEndLocation() + 1, exon.getGenomicEndLocation(), codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", exon.getExonNumber(), exon.getExonId(), GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfCDSFeature cds1 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(tmpCdsMinusStart); exon.setStartCodon(startCodon1); @@ -631,16 +588,14 @@ private static GencodeGtfExonFeature createStartCodonExon(final int exonStart, f final GencodeGtfFeatureBaseData tmpStartCodon2 = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.START_CODON, exon.getGenomicEndLocation() - length5pUtr - 2, exon.getGenomicStartLocation() + length5pUtr, codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", 1, "TEST_EXON1", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfStartCodonFeature startCodon2 = (GencodeGtfStartCodonFeature) GencodeGtfFeature.create(tmpStartCodon2); final GencodeGtfFeatureBaseData tmpCdsMinusStart2 = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, exon.getGenomicStartLocation(), startCodon2.getGenomicStartLocation() - 1, codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", exon.getExonNumber(), exon.getExonId(), GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfCDSFeature cds2 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(tmpCdsMinusStart2); exon.setStartCodon(startCodon2); @@ -658,16 +613,14 @@ private static GencodeGtfExonFeature createMiddleExon(final int exonStart, final final GencodeGtfFeatureBaseData tmpExon = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, exonStart, exonStart + lengthExons - 1, codingDirection, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", exonNum, "TEST_EXON_" + exonNum, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfExonFeature exon = (GencodeGtfExonFeature) GencodeGtfFeature.create(tmpExon); final GencodeGtfFeatureBaseData tmpCds = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum.getAndIncrement(), contig, GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, exon.getGenomicStartLocation(), exon.getGenomicEndLocation(), codingDirection, GencodeGtfFeature.GenomicPhase.DOT, exon.getGeneId(), "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, exon.getGeneName(), GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", exon.getExonNumber(), exon.getExonId(), GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfCDSFeature cds = (GencodeGtfCDSFeature) GencodeGtfFeature.create(tmpCds); exon.setCds(cds); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java index 2c3eabd08d5..32f7df59926 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java @@ -280,8 +280,8 @@ private GencodeGtfFeatureBaseData createGtfBaseDataForTestIs5Prime(final SimpleI 1, "", GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - null, - ""); + null + ); } private GencodeGtfExonFeature helpCreateExonFeature(final SimpleInterval interval, @@ -701,7 +701,7 @@ Object[][] provideForCreateDefaultFuncotationsOnProblemVariant() { data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 1, variantInterval.getContig(), GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.GENE, variantInterval.getStart()-2000, variantInterval.getEnd()+2000, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", null, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), - null, "TEST_GENE", null, null, null, -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), null, null); + null, "TEST_GENE", null, null, null, -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), null); final GencodeGtfGeneFeature gene = (GencodeGtfGeneFeature)GencodeGtfFeature.create(data); // ====================== @@ -709,8 +709,7 @@ Object[][] provideForCreateDefaultFuncotationsOnProblemVariant() { data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 2, variantInterval.getContig(), GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.TRANSCRIPT, variantInterval.getStart()-1000, variantInterval.getEnd()+1000, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "TEST_GENE1", "TEST_TRANSCRIPT1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_GENE", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "TEST_TRANSCRIPT1", -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null + Collections.emptyList() ); final GencodeGtfTranscriptFeature transcript1 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); gene.addTranscript(transcript1); diff --git a/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/EnsemblGtfCodecUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/EnsemblGtfCodecUnitTest.java index c0dcbf9fd60..c3660f3222b 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/EnsemblGtfCodecUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/EnsemblGtfCodecUnitTest.java @@ -11,6 +11,8 @@ import java.io.FileInputStream; import java.io.IOException; import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.Stream; /** * Test class for the ENSEMBL GTF Reader. @@ -30,8 +32,12 @@ private GencodeGtfFeature createEcoliEnsemblGene(final int startingFeatureOrder, final String exonId, final int cdsStart, final int cdsEnd) { // Placeholder for constant extra data: - final String geneAnonymousOptionalFields = " gene_source \"ena\";"; - final String transcriptAnonymousOptionalFields = geneAnonymousOptionalFields + " transcript_source \"ena\";"; + final List> geneAnonymousOptionalFields = Arrays.asList( new GencodeGtfFeature.OptionalField<>("gene_source", "ena")); + final List> transcriptAnonymousOptionalFields = Arrays.asList( + new GencodeGtfFeature.OptionalField<>("gene_source", "ena"), + new GencodeGtfFeature.OptionalField<>("transcript_source", "ena")); + //final String geneAnonymousOptionalFields = " gene_source \"ena\";"; + //final String transcriptAnonymousOptionalFields = geneAnonymousOptionalFields + " transcript_source \"ena\";"; int featureOrderNum = startingFeatureOrder; @@ -40,7 +46,6 @@ private GencodeGtfFeature createEcoliEnsemblGene(final int startingFeatureOrder, data = new GencodeGtfFeatureBaseData(EnsemblGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum++, ECOLI_CONTIG_NAME, GencodeGtfFeature.ANNOTATION_SOURCE_ENA, GencodeGtfFeature.FeatureType.GENE, geneStart, geneEnd, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, geneId, null, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, null, null, null, -1, null, null, - null, geneAnonymousOptionalFields); final GencodeGtfGeneFeature gene = (GencodeGtfGeneFeature)GencodeGtfFeature.create(data); gene.setUcscGenomeVersion(ECOLI_UCSC_GENOME_VERSION); @@ -48,7 +53,6 @@ private GencodeGtfFeature createEcoliEnsemblGene(final int startingFeatureOrder, data = new GencodeGtfFeatureBaseData(EnsemblGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum++, ECOLI_CONTIG_NAME, GencodeGtfFeature.ANNOTATION_SOURCE_ENA, GencodeGtfFeature.FeatureType.TRANSCRIPT, geneStart, geneEnd, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, geneId, transcriptId, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, transcriptName, -1, null, null, - null, transcriptAnonymousOptionalFields ); final GencodeGtfTranscriptFeature transcript = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); @@ -57,7 +61,6 @@ private GencodeGtfFeature createEcoliEnsemblGene(final int startingFeatureOrder, data = new GencodeGtfFeatureBaseData(EnsemblGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum++, ECOLI_CONTIG_NAME, GencodeGtfFeature.ANNOTATION_SOURCE_ENA, GencodeGtfFeature.FeatureType.EXON, geneStart, geneEnd, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, geneId, transcriptId, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, transcriptName, 1, exonId, null, - null, transcriptAnonymousOptionalFields ); final GencodeGtfExonFeature exon = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); @@ -66,8 +69,10 @@ private GencodeGtfFeature createEcoliEnsemblGene(final int startingFeatureOrder, data = new GencodeGtfFeatureBaseData(EnsemblGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum++, ECOLI_CONTIG_NAME, GencodeGtfFeature.ANNOTATION_SOURCE_ENA, GencodeGtfFeature.FeatureType.CDS, cdsStart, cdsEnd, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, geneId, transcriptId, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, transcriptName, 1, null, null, - Collections.singletonList(new GencodeGtfFeature.OptionalField<>("protein_id", transcriptId)), - transcriptAnonymousOptionalFields + Stream.concat( + transcriptAnonymousOptionalFields.stream(), + Stream.of(new GencodeGtfFeature.OptionalField<>("protein_id", transcriptId)) + ).collect(Collectors.toList()) ); final GencodeGtfCDSFeature cds = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); cds.setUcscGenomeVersion(ECOLI_UCSC_GENOME_VERSION); @@ -75,7 +80,6 @@ private GencodeGtfFeature createEcoliEnsemblGene(final int startingFeatureOrder, data = new GencodeGtfFeatureBaseData(EnsemblGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum++, ECOLI_CONTIG_NAME, GencodeGtfFeature.ANNOTATION_SOURCE_ENA, GencodeGtfFeature.FeatureType.START_CODON, cdsStart, cdsStart+2, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, geneId, transcriptId, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, transcriptName, 1, null, null, - null, transcriptAnonymousOptionalFields ); final GencodeGtfStartCodonFeature startCodon = (GencodeGtfStartCodonFeature) GencodeGtfFeature.create(data); @@ -84,7 +88,6 @@ private GencodeGtfFeature createEcoliEnsemblGene(final int startingFeatureOrder, data = new GencodeGtfFeatureBaseData(EnsemblGtfCodec.GTF_FILE_TYPE_STRING, featureOrderNum, ECOLI_CONTIG_NAME, GencodeGtfFeature.ANNOTATION_SOURCE_ENA, GencodeGtfFeature.FeatureType.STOP_CODON, cdsEnd+1, cdsEnd+3, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, geneId, transcriptId, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, geneName, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, transcriptName, 1, null, null, - null, transcriptAnonymousOptionalFields ); final GencodeGtfStopCodonFeature stopCodon = (GencodeGtfStopCodonFeature) GencodeGtfFeature.create(data); diff --git a/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodecUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodecUnitTest.java index b99f17cd94e..bb766ac1c5c 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodecUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodecUnitTest.java @@ -96,7 +96,7 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid1() { data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 6, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.GENE, 30366, 30503, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000284332.1", null, GencodeGTFFieldConstants.KnownGeneBiotype.MIRNA.toString(), - null, "MIR1302-2", null, null, null, -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), null, null); + null, "MIR1302-2", null, null, null, -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), null); final GencodeGtfGeneFeature gene = (GencodeGtfGeneFeature)GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 7, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.TRANSCRIPT, @@ -107,9 +107,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid1() { new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.NA.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfTranscriptFeature transcript = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 8, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, @@ -120,9 +119,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid1() { new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.NA.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); // ====================== @@ -156,9 +154,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() Collections.singletonList( new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfGeneFeature gene1 = (GencodeGtfGeneFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 7, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.TRANSCRIPT, 50200979, 50217615, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -171,9 +168,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfTranscriptFeature transcript1 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 8, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 50200979, 50201590, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -186,9 +182,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon1 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 9, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 50201037, 50201590, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -201,9 +196,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds1 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 10, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.START_CODON, 50201037, 50201039, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -216,9 +210,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfStartCodonFeature start_codon1 = (GencodeGtfStartCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 11, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 50206317, 50206520, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -231,9 +224,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon2 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 12, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 50206317, 50206520, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -246,9 +238,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds2 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 13, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 50208536, 50208716, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -261,9 +252,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon3 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 14, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 50208536, 50208716, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -276,9 +266,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds3 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 15, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 50210181, 50210311, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -291,9 +280,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon4 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 16, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 50210181, 50210311, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -306,9 +294,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds4 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 17, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 50210631, 50210911, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -321,9 +308,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon5 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 18, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 50210631, 50210911, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -336,9 +322,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds5 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 19, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 50215717, 50215867, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -351,9 +336,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon6 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 20, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 50215717, 50215867, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.TWO, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -366,9 +350,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds6 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 21, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 50216691, 50216876, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -381,9 +364,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon7 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 22, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 50216691, 50216876, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -396,9 +378,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds7 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 23, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 50216972, 50217128, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -411,9 +392,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon8 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 24, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 50216972, 50217128, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -426,9 +406,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds8 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 25, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 50217205, 50217357, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -441,9 +420,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon9 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 26, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 50217205, 50217357, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -456,9 +434,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds9 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 27, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 50217361, 50217615, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -471,9 +448,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon10 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 28, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 50217361, 50217366, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -486,9 +462,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds10 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 29, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.STOP_CODON, 50217367, 50217369, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -501,9 +476,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfStopCodonFeature stop_codon1 = (GencodeGtfStopCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 30, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, 50200979, 50201036, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -516,9 +490,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr1 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 31, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, 50217367, 50217615, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000611222.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -531,9 +504,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.APPRIS_ALTERNATIVE_2.toString()), new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr2 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 32, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.TRANSCRIPT, 50200979, 50217616, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -550,9 +522,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfTranscriptFeature transcript2 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 33, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.SELENOCYSTEINE, 50217358, 50217360, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -569,9 +540,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfSelenocysteineFeature selenocysteine1 = (GencodeGtfSelenocysteineFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 34, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50200979, 50201590, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -588,9 +558,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon11 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 35, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50201037, 50201590, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -607,9 +576,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds11 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 36, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.START_CODON, 50201037, 50201039, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -626,9 +594,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfStartCodonFeature start_codon2 = (GencodeGtfStartCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 37, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50206317, 50206520, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -645,9 +612,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon12 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 38, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50206317, 50206520, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -664,9 +630,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds12 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 39, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50208536, 50208716, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -683,9 +648,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon13 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 40, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50208536, 50208716, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -702,9 +666,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds13 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 41, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50210181, 50210311, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -721,9 +684,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon14 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 42, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50210181, 50210311, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -740,9 +702,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds14 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 43, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50210631, 50210911, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -759,9 +720,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon15 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 44, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50210631, 50210911, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -778,9 +738,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds15 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 45, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50215717, 50215867, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -797,9 +756,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon16 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 46, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50215717, 50215867, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.TWO, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -816,9 +774,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds16 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 47, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50216691, 50216876, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -835,9 +792,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon17 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 48, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50216691, 50216876, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -854,9 +810,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds17 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 49, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50216972, 50217128, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -873,9 +828,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon18 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 50, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50216972, 50217128, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -892,9 +846,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds18 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 51, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50217205, 50217616, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -911,9 +864,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon19 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 52, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50217205, 50217366, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -930,9 +882,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds19 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 53, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.STOP_CODON, 50217367, 50217369, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -949,9 +900,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfStopCodonFeature stop_codon2 = (GencodeGtfStopCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 54, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.UTR, 50200979, 50201036, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -968,9 +918,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr3 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 55, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.UTR, 50217367, 50217616, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000380903.6", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -987,9 +936,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr4 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 56, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.TRANSCRIPT, 50206442, 50217616, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1000,9 +948,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfTranscriptFeature transcript3 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 57, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50206442, 50206520, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1013,9 +960,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon20 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 58, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50208488, 50208716, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1026,9 +972,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon21 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 59, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50210181, 50210311, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1039,9 +984,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon22 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 60, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50210631, 50210911, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1052,9 +996,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon23 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 61, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50215717, 50215867, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1065,9 +1008,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon24 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 62, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50216691, 50216876, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1078,9 +1020,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon25 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 63, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50216972, 50217128, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1091,9 +1032,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon26 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 64, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50217205, 50217616, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.13", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1104,9 +1044,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_valid_gencode_file2() new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon27 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); // ====================== @@ -1270,7 +1209,7 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 6, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.GENE, 138082, 161852, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", null, GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), null, "AC007325.2", null, null, null, -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - new ArrayList<>(), null + new ArrayList<>() ); final GencodeGtfGeneFeature gene1 = (GencodeGtfGeneFeature) GencodeGtfFeature.create(data); @@ -1283,9 +1222,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfTranscriptFeature transcript1 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 8, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 161689, 161750, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1296,9 +1234,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon1 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 9, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 156289, 156497, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1309,9 +1246,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon2 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 10, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 156289, 156446, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1322,9 +1258,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds1 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 11, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.START_CODON, 156444, 156446, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1335,9 +1270,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfStartCodonFeature start_codon1 = (GencodeGtfStartCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 12, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 150987, 151021, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1348,9 +1282,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon3 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 13, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 150987, 151021, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1361,9 +1294,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds2 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 14, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 150350, 150499, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1374,9 +1306,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon4 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 15, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 150350, 150499, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.TWO, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1387,9 +1318,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds3 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 16, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 148414, 148478, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1400,9 +1330,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon5 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 17, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 148414, 148478, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.TWO, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1413,9 +1342,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds4 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 18, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 148116, 148232, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1426,9 +1354,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon6 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 19, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 148116, 148232, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1439,9 +1366,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds5 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 20, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 147624, 147703, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1452,9 +1378,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon7 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 21, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 147624, 147703, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1465,9 +1390,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds6 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 22, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 146640, 146721, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1478,9 +1402,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon8 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 23, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 146640, 146721, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1491,9 +1414,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds7 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 24, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 145004, 145096, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1504,9 +1426,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon9 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 25, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 145004, 145096, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1517,9 +1438,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds8 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 26, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 144749, 144895, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1530,9 +1450,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon10 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 27, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 144749, 144895, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1543,9 +1462,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds9 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 28, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 143614, 143789, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1556,9 +1474,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon11 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 29, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 143614, 143789, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1569,9 +1486,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds10 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 30, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 142194, 142292, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1582,9 +1498,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon12 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 31, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 142194, 142292, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1595,9 +1510,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds11 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 32, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 138743, 138831, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1608,9 +1522,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon13 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 33, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 138743, 138831, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1621,9 +1534,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds12 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 34, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 138082, 138667, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1634,9 +1546,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon14 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 35, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 138483, 138667, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.TWO, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1647,9 +1558,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds13 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 36, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.STOP_CODON, 138480, 138482, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1660,9 +1570,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfStopCodonFeature stop_codon1 = (GencodeGtfStopCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 37, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, 161689, 161750, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1673,9 +1582,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr1 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 38, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, 156447, 156497, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1686,9 +1594,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr2 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 39, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, 138082, 138482, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000615165.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1699,9 +1606,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr3 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 40, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.TRANSCRIPT, 138082, 161852, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1712,9 +1618,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfTranscriptFeature transcript2 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 41, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 161689, 161852, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1725,9 +1630,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon15 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 42, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 161314, 161626, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1738,9 +1642,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon16 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 43, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 161314, 161586, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1751,9 +1654,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds14 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 44, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.START_CODON, 161584, 161586, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1764,9 +1666,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfStartCodonFeature start_codon2 = (GencodeGtfStartCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 45, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 156289, 156497, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1777,9 +1678,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon17 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 46, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 156289, 156497, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1790,9 +1690,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds15 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 47, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 150987, 151021, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1803,9 +1702,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon18 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 48, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 150987, 151021, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1816,9 +1714,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds16 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 49, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 150350, 150499, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1829,9 +1726,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon19 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 50, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 150350, 150499, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.TWO, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1842,9 +1738,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds17 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 51, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 148414, 148478, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1855,9 +1750,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon20 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 52, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 148414, 148478, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.TWO, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1868,9 +1762,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds18 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 53, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 148116, 148232, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1881,9 +1774,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon21 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 54, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 148116, 148232, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1894,9 +1786,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds19 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 55, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 147624, 147703, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1907,9 +1798,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon22 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 56, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 147624, 147703, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1920,9 +1810,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds20 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 57, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 146640, 146721, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1933,9 +1822,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon23 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 58, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 146640, 146721, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1946,9 +1834,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds21 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 59, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 145004, 145096, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1959,9 +1846,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon24 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 60, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 145004, 145096, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1972,9 +1858,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds22 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 61, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 144749, 144895, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1985,9 +1870,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon25 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 62, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 144749, 144895, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -1998,9 +1882,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds23 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 63, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 143614, 143789, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2011,9 +1894,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon26 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 64, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 143614, 143789, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2024,9 +1906,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds24 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 65, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 142194, 142292, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2037,9 +1918,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon27 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 66, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 142194, 142292, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2050,9 +1930,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds25 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 67, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 138743, 138831, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2063,9 +1942,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon28 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 68, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 138743, 138831, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2076,9 +1954,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds26 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 69, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, 138082, 138667, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2089,9 +1966,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon29 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 70, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, 138483, 138667, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.TWO, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2102,9 +1978,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds27 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 71, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.STOP_CODON, 138480, 138482, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2115,9 +1990,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfStopCodonFeature stop_codon2 = (GencodeGtfStopCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 72, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, 161689, 161852, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2128,9 +2002,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr4 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 73, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, 161587, 161626, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2141,9 +2014,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr5 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 74, "KI270734.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, 138082, 138482, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000277196.4", "ENST00000621424.4", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2154,9 +2026,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_and_this_is_a_valid_o new GencodeGtfFeature.OptionalField("transcript_support_level", GencodeGTFFieldConstants.TranscriptSupportLevel.ALL_MRNA_VERIFIED.toString()), new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr6 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); // ====================== @@ -2336,9 +2207,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_valid_file1() { Collections.singletonList( new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000000961.2") ) - ), - null - ); + ) + ); final GencodeGtfGeneFeature gene = (GencodeGtfGeneFeature)GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 7, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.TRANSCRIPT, @@ -2351,9 +2221,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_valid_file1() { new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000000961.2"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000362751.1") ) - ), - null - ); + ) + ); final GencodeGtfTranscriptFeature transcript = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 8, "chr1", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, @@ -2366,9 +2235,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_valid_file1() { new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000000961.2"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000362751.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); // ====================== @@ -2398,9 +2266,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ Collections.singletonList( new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000186123.2") ) - ), - null - ); + ) + ); final GencodeGtfGeneFeature gene1 = (GencodeGtfGeneFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 7, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.TRANSCRIPT, 50637519, 50638976, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000273253.1", "ENST00000608025.1", GencodeGTFFieldConstants.KnownGeneBiotype.ANTISENSE.toString(), @@ -2411,9 +2278,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000186123.2"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000472292.2") ) - ), - null - ); + ) + ); final GencodeGtfTranscriptFeature transcript1 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 8, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50638505, 50638976, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000273253.1", "ENST00000608025.1", GencodeGTFFieldConstants.KnownGeneBiotype.ANTISENSE.toString(), @@ -2424,9 +2290,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000186123.2"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000472292.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon1 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 9, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50637519, 50637757, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000273253.1", "ENST00000608025.1", GencodeGTFFieldConstants.KnownGeneBiotype.ANTISENSE.toString(), @@ -2437,9 +2302,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000186123.2"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000472292.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon2 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 10, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.GENE, 50639408, 50656045, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENSG00000073169.9", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2448,9 +2312,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ Collections.singletonList( new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3") ) - ), - null - ); + ) + ); final GencodeGtfGeneFeature gene2 = (GencodeGtfGeneFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 11, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.TRANSCRIPT, 50639408, 50656045, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2465,9 +2328,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfTranscriptFeature transcript2 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 12, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.SELENOCYSTEINE, 50655787, 50655789, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2482,9 +2344,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfSelenocysteineFeature selenocysteine1 = (GencodeGtfSelenocysteineFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 13, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50639408, 50640019, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2499,9 +2360,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon3 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 14, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50639466, 50640019, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2516,9 +2376,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds1 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 15, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.START_CODON, 50639466, 50639468, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2533,9 +2392,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfStartCodonFeature start_codon1 = (GencodeGtfStartCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 16, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50644746, 50644949, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2550,9 +2408,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon4 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 17, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50644746, 50644949, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2567,9 +2424,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds2 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 18, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50646965, 50647145, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2584,9 +2440,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon5 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 19, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50646965, 50647145, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2601,9 +2456,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds3 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 20, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50648610, 50648740, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2618,9 +2472,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon6 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 21, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50648610, 50648740, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2635,9 +2488,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds4 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 22, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50649060, 50649340, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2652,9 +2504,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon7 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 23, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50649060, 50649340, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2669,9 +2520,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds5 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 24, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50654146, 50654296, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2686,9 +2536,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon8 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 25, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50654146, 50654296, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.TWO, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2703,9 +2552,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds6 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 26, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50655120, 50655305, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2720,9 +2568,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon9 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 27, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50655120, 50655305, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2737,9 +2584,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds7 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 28, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50655401, 50655557, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2754,9 +2600,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon10 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 29, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50655401, 50655557, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ONE, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2771,9 +2616,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds8 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 30, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50655634, 50656045, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2788,9 +2632,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon11 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 31, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.CDS, 50655634, 50655795, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2805,9 +2648,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds9 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 32, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.STOP_CODON, 50655796, 50655798, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.ZERO, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2822,9 +2664,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfStopCodonFeature stop_codon1 = (GencodeGtfStopCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 33, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.UTR, 50639408, 50639465, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2839,9 +2680,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr1 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 34, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.UTR, 50655796, 50656045, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000380903.2", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2856,9 +2696,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000075003.2") ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr2 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 35, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.TRANSCRIPT, 50644871, 50656045, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2869,9 +2708,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfTranscriptFeature transcript3 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 36, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50644871, 50644949, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2882,9 +2720,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon12 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 37, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50646917, 50647145, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2895,9 +2732,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon13 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 38, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50648610, 50648740, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2908,9 +2744,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon14 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 39, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50649060, 50649340, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2921,9 +2756,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon15 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 40, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50654146, 50654296, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2934,9 +2768,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon16 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 41, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50655120, 50655305, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2947,9 +2780,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon17 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 42, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50655401, 50655557, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2960,9 +2792,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon18 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 43, "chr22", GencodeGtfFeature.ANNOTATION_SOURCE_HAVANA, GencodeGtfFeature.FeatureType.EXON, 50655634, 50656045, Strand.POSITIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000073169.9", "ENST00000492092.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), @@ -2973,9 +2804,8 @@ private ArrayList createGencodeGtfGene_gencode_v19_valid_ new GencodeGtfFeature.OptionalField("havana_gene", "OTTHUMG00000044645.3"), new GencodeGtfFeature.OptionalField("havana_transcript", "OTTHUMT00000316993.1") ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon19 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); // ====================== @@ -3087,8 +2917,7 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 6, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.GENE, 38792, 97421, Strand.NEGATIVE, GencodeGtfFeature.GenomicPhase.DOT, "ENSG00000215615.1", "ENSG00000215615.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), GencodeGTFFieldConstants.GeneTranscriptStatus.KNOWN.toString(), "AL354822.1", GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString(), GencodeGTFFieldConstants.GeneTranscriptStatus.KNOWN.toString(), "AL354822.1", -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - new ArrayList<>(), null - ); + new ArrayList<>() ); final GencodeGtfGeneFeature gene1 = (GencodeGtfGeneFeature) GencodeGtfFeature.create(data); @@ -3099,9 +2928,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfTranscriptFeature transcript1 = (GencodeGtfTranscriptFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 8, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, @@ -3111,9 +2939,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon1 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 9, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, @@ -3123,9 +2950,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon2 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 10, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, @@ -3135,9 +2961,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds1 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 11, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.START_CODON, @@ -3147,9 +2972,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfStartCodonFeature start_codon1 = (GencodeGtfStartCodonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 12, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, @@ -3159,9 +2983,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon3 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 13, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, @@ -3171,9 +2994,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds2 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 14, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, @@ -3183,9 +3005,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon4 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 15, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, @@ -3195,9 +3016,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds3 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 16, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.EXON, @@ -3207,9 +3027,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfExonFeature exon5 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 17, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.CDS, @@ -3219,9 +3038,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfCDSFeature cds4 = (GencodeGtfCDSFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 18, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, @@ -3231,9 +3049,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr1 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 19, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, @@ -3243,9 +3060,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr2 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); data = new GencodeGtfFeatureBaseData(GencodeGtfCodec.GTF_FILE_TYPE_STRING, 20, "GL000218.1", GencodeGtfFeature.ANNOTATION_SOURCE_ENSEMBL, GencodeGtfFeature.FeatureType.UTR, @@ -3255,9 +3071,8 @@ private GencodeGtfGeneFeature createGencodeGtfGene_gencode_v19_and_this_is_a_val Collections.singletonList( new GencodeGtfFeature.OptionalField("tag", GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) ) - ), - null - ); + ) + ); final GencodeGtfUTRFeature utr3 = (GencodeGtfUTRFeature) GencodeGtfFeature.create(data); // ====================== diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/FuncotatorTestUtils.java b/src/test/java/org/broadinstitute/hellbender/utils/test/FuncotatorTestUtils.java index 167e3ec3874..b97e2d27af8 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/FuncotatorTestUtils.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/test/FuncotatorTestUtils.java @@ -299,8 +299,8 @@ public static GencodeGtfTranscriptFeature createArtificialGencodeGtfTranscriptFe -1, null, GencodeGTFFieldConstants.LocusLevel.AUTOMATICALLY_ANNOTATED.toString(), - Collections.emptyList(), - null) + Collections.emptyList() + ) ); }