ADAM_2.12: Core 1.0 API < Back
 

# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package algorithms
  Definition Classes
    adam
-  package converters
  Definition Classes
    adam
-  package ds
  Definition Classes
    adam
-  package io
  Definition Classes
    adam
-  package models
  Definition Classes
    adam
-  package projections
  Definition Classes
    adam
-  package rich
  Definition Classes
    adam
-  package serialization
  Definition Classes
    adam
-  package sql
  Definition Classes
    adam
- Alignment
- Dbxref
- Feature
- Fragment
- Genotype
- OntologyTerm
- ProcessingStep
- Read
- Reference
- Sequence
- Slice
- TranscriptEffect
- Variant
- VariantAnnotation
- VariantCallingAnnotations
- VariantContext
-  package util
  Definition Classes
    adam

p

org.bdgenomics.adam

# sql 

#### package sql

 
Ordering

1. Alphabetic

Visibility

1. Public
2. All

### 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