Packages

package sql

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Visibility
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Type Members

  1. case class Alignment(referenceName: Option[String] = None, start: Option[Long] = None, originalStart: Option[Long] = None, end: Option[Long] = None, mappingQuality: Option[Int] = None, readName: Option[String] = None, sequence: Option[String] = None, qualityScores: Option[String] = None, cigar: Option[String] = None, originalCigar: Option[String] = None, basesTrimmedFromStart: Option[Int] = None, basesTrimmedFromEnd: Option[Int] = None, readPaired: Option[Boolean] = None, properPair: Option[Boolean] = None, readMapped: Option[Boolean] = None, mateMapped: Option[Boolean] = None, failedVendorQualityChecks: Option[Boolean] = None, duplicateRead: Option[Boolean] = None, readNegativeStrand: Option[Boolean] = None, mateNegativeStrand: Option[Boolean] = None, primaryAlignment: Option[Boolean] = None, secondaryAlignment: Option[Boolean] = None, supplementaryAlignment: Option[Boolean] = None, mismatchingPositions: Option[String] = None, originalQualityScores: Option[String] = None, readGroupId: Option[String] = None, readGroupSampleId: Option[String] = None, mateAlignmentStart: Option[Long] = None, mateReferenceName: Option[String] = None, insertSize: Option[Long] = None, readInFragment: Option[Int] = None, attributes: Option[String] = None) extends Product with Serializable
  2. case class Dbxref(db: Option[String] = None, accession: Option[String] = None) extends Product with Serializable
  3. case class Feature(featureId: Option[String] = None, sampleId: Option[String] = None, name: Option[String] = None, source: Option[String] = None, featureType: Option[String] = None, referenceName: Option[String] = None, start: Option[Long] = None, end: Option[Long] = None, strand: Option[String] = None, phase: Option[Int] = None, frame: Option[Int] = None, score: Option[Double] = None, geneId: Option[String] = None, transcriptId: Option[String] = None, exonId: Option[String] = None, proteinId: Option[String] = None, aliases: Seq[String] = Seq(), parentIds: Seq[String] = Seq(), target: Option[String] = None, gap: Option[String] = None, derivesFrom: Option[String] = None, notes: Seq[String] = Seq(), dbxrefs: Seq[Dbxref] = Seq(), ontologyTerms: Seq[OntologyTerm] = Seq(), circular: Option[Boolean] = None, attributes: Map[String, String] = Map()) extends Product with Serializable
  4. case class Fragment(name: Option[String] = None, readGroupId: Option[String] = None, insertSize: Option[Int] = None, alignments: Seq[Alignment] = Seq()) extends Product with Serializable
  5. case class Genotype(variant: Option[Variant] = None, referenceName: Option[String] = None, start: Option[Long] = None, end: Option[Long] = None, variantCallingAnnotations: Option[VariantCallingAnnotations] = None, sampleId: Option[String] = None, sampleDescription: Option[String] = None, processingDescription: Option[String] = None, alleles: Seq[String] = Seq(), expectedAlleleDosage: Option[Float] = None, referenceReadDepth: Option[Int] = None, alternateReadDepth: Option[Int] = None, readDepth: Option[Int] = None, minReadDepth: Option[Int] = None, genotypeQuality: Option[Int] = None, genotypeLikelihoods: Seq[Double] = Seq(), nonReferenceLikelihoods: Seq[Double] = Seq(), strandBiasComponents: Seq[Int] = Seq(), splitFromMultiAllelic: Option[Boolean] = None, phased: Option[Boolean] = None, phaseSetId: Option[Int] = None, phaseQuality: Option[Int] = None) extends Product with Serializable
  6. case class OntologyTerm(db: Option[String] = None, accession: Option[String] = None) extends Product with Serializable
  7. case class ProcessingStep(id: Option[String] = None, programName: Option[String] = None, commandLine: Option[String] = None, previousId: Option[String] = None, description: Option[String] = None, version: Option[String] = None) extends Product with Serializable
  8. case class Read(name: Option[String] = None, description: Option[String] = None, alphabet: Option[String] = None, sequence: Option[String] = None, length: Option[Long] = None, qualityScores: Option[String] = None, sampleId: Option[String] = None, attributes: Map[String, String] = Map()) extends Product with Serializable
  9. case class Reference(name: Option[String] = None, length: Option[Long] = None, md5: Option[String] = None, sourceUri: Option[String] = None, assembly: Option[String] = None, sourceAccessions: Seq[String] = Seq(), species: Option[String] = None, index: Option[Int] = None) extends Product with Serializable
  10. case class Sequence(name: Option[String] = None, description: Option[String] = None, alphabet: Option[String] = None, sequence: Option[String] = None, length: Option[Long] = None, sampleId: Option[String] = None, attributes: Map[String, String] = Map()) extends Product with Serializable
  11. case class Slice(name: Option[String] = None, description: Option[String] = None, alphabet: Option[String] = None, sequence: Option[String] = None, start: Option[Long] = None, end: Option[Long] = None, strand: Option[String] = None, length: Option[Long] = None, totalLength: Option[Long] = None, index: Option[Int] = None, slices: Option[Int] = None, sampleId: Option[String] = None, attributes: Map[String, String] = Map()) extends Product with Serializable
  12. case class TranscriptEffect(alternateAllele: Option[String] = None, effects: Seq[String] = Seq(), impact: Option[String] = None, geneName: Option[String] = None, geneId: Option[String] = None, featureType: Option[String] = None, featureId: Option[String] = None, biotype: Option[String] = None, strand: Option[String] = None, rank: Option[Int] = None, total: Option[Int] = None, genomicHgvs: Option[String] = None, transcriptHgvs: Option[String] = None, proteinHgvs: Option[String] = None, cdnaPosition: Option[Int] = None, cdnaLength: Option[Int] = None, codingSequencePosition: Option[Int] = None, codingSequenceLength: Option[Int] = None, referenceCodingSequence: Option[String] = None, alternateCodingSequence: Option[String] = None, proteinPosition: Option[Int] = None, proteinLength: Option[Int] = None, referenceProteinSequence: Option[String] = None, alternateProteinSequence: Option[String] = None, distance: Option[Int] = None, messages: Seq[String] = Seq()) extends Product with Serializable
  13. case class Variant(referenceName: Option[String] = None, start: Option[Long] = None, end: Option[Long] = None, names: Seq[String] = Seq(), splitFromMultiAllelic: Option[Boolean] = None, referenceAllele: Option[String] = None, alternateAllele: Option[String] = None, quality: Option[Double] = None, filtersApplied: Option[Boolean] = None, filtersPassed: Option[Boolean] = None, filtersFailed: Seq[String] = Seq(), annotation: Option[VariantAnnotation] = None) extends Product with Serializable
  14. case class VariantAnnotation(ancestralAllele: Option[String] = None, alleleCount: Option[Int] = None, readDepth: Option[Int] = None, forwardReadDepth: Option[Int] = None, reverseReadDepth: Option[Int] = None, referenceReadDepth: Option[Int] = None, referenceForwardReadDepth: Option[Int] = None, referenceReverseReadDepth: Option[Int] = None, alleleFrequency: Option[Float] = None, cigar: Option[String] = None, dbSnp: Option[Boolean] = None, hapMap2: Option[Boolean] = None, hapMap3: Option[Boolean] = None, validated: Option[Boolean] = None, thousandGenomes: Option[Boolean] = None, somatic: Option[Boolean] = None, transcriptEffects: Seq[TranscriptEffect] = Seq(), attributes: Map[String, String] = Map()) extends Product with Serializable
  15. case class VariantCallingAnnotations(filtersApplied: Option[Boolean] = None, filtersPassed: Option[Boolean] = None, filtersFailed: Seq[String] = Seq(), downsampled: Option[Boolean] = None, baseQRankSum: Option[Float] = None, fisherStrandBiasPValue: Option[Float] = None, rmsMapQ: Option[Float] = None, mapq0Reads: Option[Int] = None, mqRankSum: Option[Float] = None, readPositionRankSum: Option[Float] = None, genotypePriors: Seq[Float] = Seq(), genotypePosteriors: Seq[Float] = Seq(), vqslod: Option[Float] = None, culprit: Option[String] = None, attributes: Map[String, String] = Map()) extends Product with Serializable
  16. case class VariantContext(referenceName: String, start: Long, end: Long, variant: Variant, genotypes: Seq[Genotype]) extends Product with Serializable

Value Members

  1. object Alignment extends Serializable
  2. object Dbxref extends Serializable
  3. object Feature extends Serializable
  4. object Fragment extends Serializable
  5. object Genotype extends Serializable
  6. object OntologyTerm extends Serializable
  7. object ProcessingStep extends Serializable
  8. object Read extends Serializable
  9. object Reference extends Serializable
  10. object Sequence extends Serializable
  11. object Slice extends Serializable
  12. object TranscriptEffect extends Serializable
  13. object Variant extends Serializable
  14. object VariantAnnotation extends Serializable
  15. object VariantCallingAnnotations extends Serializable
  16. object VariantContext extends Serializable

Ungrouped