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

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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