| Class | Description |
|---|---|
| AbstractGtfCodec | |
| EnsemblGtfCodec |
Codec to decode data in GTF format from ENSEMBL.
|
| GencodeGtfCDSFeature |
A Gencode GTF Feature representing a CDS.
|
| GencodeGtfCodec |
Tribble Codec to read data from a GENCODE GTF file. |
| GencodeGtfExonFeature |
A Gencode GTF Feature representing an exon.
|
| GencodeGtfFeature |
A
GencodeGtfFeature represents data in a GENCODE GTF file. |
| GencodeGtfFeature.OptionalField<T> | |
| GencodeGtfFeatureBaseData |
Struct-like container class for the fields in a
GencodeGtfFeature
This is designed to be a basic dummy class to make feature instantiation easier. |
| GencodeGtfGeneFeature |
A Gencode GTF Feature representing a gene.
|
| GencodeGtfSelenocysteineFeature |
A Gencode GTF Feature representing a selenocysteine.
|
| GencodeGtfStartCodonFeature |
A Gencode GTF Feature representing a start codon.
|
| GencodeGtfStopCodonFeature |
A Gencode GTF Feature representing a stop codon.
|
| GencodeGtfTranscriptFeature |
A Gencode GTF Feature representing a transcript.
|
| GencodeGtfUTRFeature |
A Gencode GTF Feature representing an untranslated region.
|
| Enum | Description |
|---|---|
| GencodeGtfFeature.AnnotationSource |
Keyword identifying the source of the feature, like a program
(e.g.
|
| GencodeGtfFeature.FeatureTag |
Additional relevant information appended to a feature.
|
| GencodeGtfFeature.FeatureType |
Type of the feature represented in a single line of a GENCODE GTF File.
|
| GencodeGtfFeature.GeneTranscriptStatus |
Indication of whether a feature is new, tenatative, or already known.
|
| GencodeGtfFeature.GeneTranscriptType |
Biotype / transcript type for the transcript or gene represented in a feature.
|
| GencodeGtfFeature.GenomicPhase |
Whether the first base of the CDS segment is the first (frame 0), second (frame 1) or third (frame 2) \
in the codon of the ORF.
|
| GencodeGtfFeature.LocusLevel |
Status of how a position was annotated / verified:
1 - verified locus
2 - manually annotated locus
3 - automatically annotated locus
For more information, see:
https://www.gencodegenes.org/data_format.html
https://en.wikipedia.org/wiki/General_feature_format
|
| GencodeGtfFeature.RemapStatus |
Attribute that indicates the status of the mapping.
|
| GencodeGtfFeature.RemapTargetStatus |
Attribute that compares the mapping to the existing target annotations.
|
| GencodeGtfFeature.TranscriptSupportLevel |
Transcript score according to how well mRNA and EST alignments match over its full length.
|