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com.fulcrumgenomics.util

GeneAnnotations

object GeneAnnotations

Stores classes useful for storing annotation information for genes and their transcripts and exons.

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  1. case class Exon (start: Int, end: Int) extends Product with Serializable

    Defines an exonic sequence within a transcript.

  2. 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.

  3. 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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