ADAM_2.12: Core 1.0.1 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package sql
  Definition Classes
    adam
- Alignment
- Dbxref
- Feature
- Fragment
- Genotype
- OntologyTerm
- ProcessingStep
- Read
- Reference
- Sequence
- Slice
- TranscriptEffect
- Variant
- VariantAnnotation
- VariantCallingAnnotations
- VariantContext

c

org.bdgenomics.adam.sql

# Alignment 

###
Companion object Alignment

#### 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

Linear Supertypes
Serializable, Serializable, Product, Equals, AnyRef, Any
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Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. Alignment
2. Serializable
3. Serializable
4. Product
5. Equals
6. AnyRef
7. Any

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Visibility

1. Public
2. All

### Instance Constructors

1.  new 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)

### Value Members

1.  final def !=(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
2.  final def ##(): Int
   Definition Classes
     AnyRef → Any
3.  final def ==(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
4.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
5.  val attributes: Option[String]
6.  val basesTrimmedFromEnd: Option[Int]
7.  val basesTrimmedFromStart: Option[Int]
8.  def canEqual(that: Any): Boolean
   Definition Classes
     Alignment → Equals
9.  val cigar: Option[String]
10.  def clone(): AnyRef
    Attributes
      protected[lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native() @HotSpotIntrinsicCandidate()
11.  val duplicateRead: Option[Boolean]
12.  val end: Option[Long]
13.  final def eq(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
14.  val failedVendorQualityChecks: Option[Boolean]
15.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
16.  val insertSize: Option[Long]
17.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
18.  val mappingQuality: Option[Int]
19.  val mateAlignmentStart: Option[Long]
20.  val mateMapped: Option[Boolean]
21.  val mateNegativeStrand: Option[Boolean]
22.  val mateReferenceName: Option[String]
23.  val mismatchingPositions: Option[String]
24.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
25.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
26.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
27.  val originalCigar: Option[String]
28.  val originalQualityScores: Option[String]
29.  val originalStart: Option[Long]
30.  val primaryAlignment: Option[Boolean]
31.  def productArity: Int
    Definition Classes
      Alignment → Product
32.  def productElement(i: Int): Any
    Definition Classes
      Alignment → Product
33.  val properPair: Option[Boolean]
34.  val qualityScores: Option[String]
35.  val readGroupId: Option[String]
36.  val readGroupSampleId: Option[String]
37.  val readInFragment: Option[Int]
38.  val readMapped: Option[Boolean]
39.  val readName: Option[String]
40.  val readNegativeStrand: Option[Boolean]
41.  val readPaired: Option[Boolean]
42.  val referenceName: Option[String]
43.  val secondaryAlignment: Option[Boolean]
44.  val sequence: Option[String]
45.  val start: Option[Long]
46.  val supplementaryAlignment: Option[Boolean]
47.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
48.  def toAvro: formats.avro.Alignment
49.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
50.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
51.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Deprecated Value Members

1.  def finalize(): Unit
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] ) @Deprecated
   Deprecated

### Inherited from Serializable

### Inherited from Product

### Inherited from Equals

### Inherited from AnyRef

### Inherited from Any

### Ungrouped