object GeneAnnotations
Stores classes useful for storing annotation information for genes and their transcripts and exons.
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case class
Exon
(start: Int, end: Int) extends Product with Serializable
Defines an exonic sequence within a transcript.
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case class
Gene
(contig: String, start: Int, end: Int, negativeStrand: Boolean, name: String, transcripts: Seq[Transcript]) extends Interval with Iterable[Transcript] with Product with Serializable
A gene with zero or more transcripts, that all are on the same transcription strand.
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case class
Transcript
(name: String, start: Int, end: Int, cdsStart: Int, cdsEnd: Int, exons: Seq[Exon]) extends Product with Serializable
A transcript associated with a given gene (which stores the transcription strand).
A transcript associated with a given gene (which stores the transcription strand). Contains zero or more exons. The exons should be given in transcript order.
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