org.bdgenomics.adam

# sql

#### package sql

Visibility

1. Public
2. All

### Type Members

1. #### case class AlignmentRecord(readInFragment: Option[Int] = None, contigName: Option[String] = None, start: Option[Long] = None, oldPosition: Option[Long] = None, end: Option[Long] = None, mapq: Option[Int] = None, readName: Option[String] = None, sequence: Option[String] = None, qual: Option[String] = None, cigar: Option[String] = None, oldCigar: 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, origQual: Option[String] = None, attributes: Option[String] = None, recordGroupName: Option[String] = None, recordGroupSample: Option[String] = None, mateAlignmentStart: Option[Long] = None, mateContigName: Option[String] = None, inferredInsertSize: Option[Long] = None) extends Product with Serializable

2. #### case class Contig(contigName: Option[String] = None, contigLength: Option[Long] = None, contigMD5: Option[String] = None, referenceURL: Option[String] = None, assembly: Option[String] = None, species: Option[String] = None, referenceIndex: Option[Int] = None) extends Product with Serializable

3. #### case class Dbxref(db: Option[String] = None, accession: Option[String] = None) extends Product with Serializable

4. #### case class Feature(featureId: Option[String] = None, sampleId: Option[String] = None, name: Option[String] = None, source: Option[String] = None, featureType: Option[String] = None, contigName: 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, 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

5. #### case class Fragment(name: Option[String] = None, recordGroupName: Option[String] = None, insertSize: Option[Int] = None, alignments: Seq[AlignmentRecord] = Seq()) extends Product with Serializable

6. #### case class Genotype(variant: Option[Variant] = None, contigName: 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

7. #### case class NucleotideContigFragment(contigName: Option[String] = None, contigLength: Option[Long] = None, description: Option[String] = None, sequence: Option[String] = None, index: Option[Int] = None, start: Option[Long] = None, end: Option[Long] = None, length: Option[Long] = None, fragments: Option[Int] = None) extends Product with Serializable

8. #### case class OntologyTerm(db: Option[String] = None, accession: Option[String] = None) extends Product with Serializable

9. #### 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

10. #### case class TranscriptEffect(alternateAllele: Option[String] = None, effects: Seq[String] = Seq(), geneName: Option[String] = None, geneId: Option[String] = None, featureType: Option[String] = None, featureId: Option[String] = None, biotype: 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, cdsPosition: Option[Int] = None, cdsLength: Option[Int] = None, proteinPosition: Option[Int] = None, proteinLength: Option[Int] = None, distance: Option[Int] = None, messages: Seq[String] = Seq()) extends Product with Serializable

11. #### case class Variant(contigName: 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

12. #### 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

13. #### 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

14. #### case class VariantContext(contigName: String, start: Long, end: Long, variant: Variant, genotypes: Seq[Genotype]) extends Product with Serializable

### Value Members

1. #### object AlignmentRecord extends Serializable

2. #### object Contig extends Serializable

3. #### object Dbxref extends Serializable

4. #### object Feature extends Serializable

5. #### object Fragment extends Serializable

6. #### object Genotype extends Serializable

7. #### object NucleotideContigFragment extends Serializable

8. #### object OntologyTerm extends Serializable

9. #### object ProcessingStep extends Serializable

10. #### object TranscriptEffect extends Serializable

11. #### object Variant extends Serializable

12. #### object VariantAnnotation extends Serializable

13. #### object VariantCallingAnnotations extends Serializable

14. #### object VariantContext extends Serializable

### Ungrouped