package genomicimplicits

Type Members

  1. case class AlleleDepthOutput(ad_ref: Int = 0, ad_alt: Int = 0, ad_total: Int = 0, ad_ratio: Double = 0) extends Product with Serializable
  2. case class CompoundHetInput(patient_id: String, chromosome: String, start: Long, reference: String, alternate: String, symbols: Seq[String], parental_origin: Option[String] = None, zygosity: String = "HET") extends Product with Serializable
  3. case class CompoundHetOutput(patient_id: String, chromosome: String, start: Long, reference: String, alternate: String, is_hc: Boolean, hc_complement: Seq[HCComplement]) extends Product with Serializable
  4. case class ConsequencesInput(chromosome: String = "1", start: Long = 1, reference: String = "T", alternate: String = "C", ensembl_transcript_id: String = "ENST00000000001", impact_score: Int = 1, symbol: String = "OR4F5", biotype: String = "protein_coding", mane_select: Boolean = false, mane_plus: Boolean = false, canonical: Boolean = false) extends Product with Serializable
  5. case class FullCompoundHetOutput(patient_id: String, chromosome: String, start: Long, reference: String, alternate: String, is_hc: Boolean, hc_complement: Seq[HCComplement], is_possibly_hc: Boolean, possibly_hc_complement: Seq[PossiblyHCComplement]) extends Product with Serializable
  6. case class Genotype(calls: Array[Int]) extends Product with Serializable
  7. case class HCComplement(symbol: String, locus: Seq[String]) extends Product with Serializable
  8. case class OtherCompoundHetInput(other_patient_id: String, chromosome: String, start: Long, reference: String, alternate: String, other_symbols: Seq[String], parental_origin: Option[String] = None, zygosity: String = "HET") extends Product with Serializable
  9. case class PickedConsequencesOuput(chromosome: String = "1", start: Long = 1, reference: String = "T", alternate: String = "C", ensembl_transcript_id: String = "ENST00000000001", impact_score: Int = 1, symbol: String = "OR4F5", biotype: String = "protein_coding", mane_select: Boolean = false, mane_plus: Boolean = false, canonical: Boolean = false, picked: Option[Boolean] = Some(true)) extends Product with Serializable
  10. case class PossiblyCompoundHetOutput(patient_id: String, chromosome: String, start: Long, reference: String, alternate: String, is_possibly_hc: Boolean, possibly_hc_complement: Seq[PossiblyHCComplement]) extends Product with Serializable
  11. case class PossiblyHCComplement(symbol: String, count: Long) extends Product with Serializable
  12. case class RefSeqAnnotation(RefSeq: Option[String] = Some("123&456")) extends Product with Serializable
  13. case class RefSeqAnnotationWithoutRefSeq(another: Option[String] = Some("test")) extends Product with Serializable
  14. case class RefSeqMrnaIdInput(id: String = "1", annotation: Option[RefSeqAnnotation] = Some(RefSeqAnnotation())) extends Product with Serializable
  15. case class RefSeqMrnaIdInputWithoutAnnotation(id: String = "1", another: String = "test") extends Product with Serializable
  16. case class RefSeqMrnaIdInputWithoutRefSeq(id: String = "1", annotation: Option[RefSeqAnnotationWithoutRefSeq] = ...) extends Product with Serializable
  17. case class RelativesGenotype(chromosome: String = "1", start: Long = 1000, reference: String = "A", alternate: String = "T", participant_id: String = "PT_1", mother_id: Option[String] = None, father_id: Option[String] = None, family_id: Option[String] = None, calls: Seq[Int] = Seq(0, 0), gq: Int = 20, other: Option[String] = None) extends Product with Serializable
  18. case class RelativesGenotypeOutput(chromosome: String = "1", start: Long = 1000, reference: String = "A", alternate: String = "T", participant_id: String = "PT_1", mother_id: Option[String] = None, father_id: Option[String] = None, family_id: Option[String] = None, calls: Seq[Int] = Seq(0, 0), gq: Int = 20, other: Option[String] = None, mother_calls: Option[Seq[Int]] = None, mother_gq: Option[Int] = None, mother_other: Option[String] = None, father_calls: Option[Seq[Int]] = None, father_gq: Option[Int] = None, father_other: Option[String] = None) extends Product with Serializable

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