Class/Object

org.bdgenomics.adam.sql

AlignmentRecord

Related Docs: object AlignmentRecord | package sql

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case class AlignmentRecord(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. AlignmentRecord
  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 AlignmentRecord(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)

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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. val attributes: Option[String]

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  6. val basesTrimmedFromEnd: Option[Int]

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  7. val basesTrimmedFromStart: Option[Int]

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  8. def canEqual(that: Any): Boolean

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    Definition Classes
    AlignmentRecord → Equals

  9. val cigar: Option[String]

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  10. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  11. val duplicateRead: Option[Boolean]

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  12. val end: Option[Long]

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  13. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  14. val failedVendorQualityChecks: Option[Boolean]

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  15. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  16. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  17. val insertSize: Option[Long]

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  18. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  19. val mappingQuality: Option[Int]

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  20. val mateAlignmentStart: Option[Long]

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  21. val mateMapped: Option[Boolean]

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  22. val mateNegativeStrand: Option[Boolean]

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  23. val mateReferenceName: Option[String]

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  24. val mismatchingPositions: Option[String]

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  25. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  26. final def notify(): Unit

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    Definition Classes
    AnyRef

  27. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  28. val originalCigar: Option[String]

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  29. val originalQualityScores: Option[String]

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  30. val originalStart: Option[Long]

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  31. val primaryAlignment: Option[Boolean]

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  32. def productArity: Int

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    Definition Classes
    AlignmentRecord → Product

  33. def productElement(i: Int): Any

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    Definition Classes
    AlignmentRecord → Product

  34. val properPair: Option[Boolean]

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  35. val qualityScores: Option[String]

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  36. val readGroupId: Option[String]

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  37. val readGroupSampleId: Option[String]

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  38. val readInFragment: Option[Int]

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  39. val readMapped: Option[Boolean]

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  40. val readName: Option[String]

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  41. val readNegativeStrand: Option[Boolean]

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  42. val readPaired: Option[Boolean]

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  43. val referenceName: Option[String]

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  44. val secondaryAlignment: Option[Boolean]

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  45. val sequence: Option[String]

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  46. val start: Option[Long]

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  47. val supplementaryAlignment: Option[Boolean]

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  48. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef

  49. def toAvro: formats.avro.AlignmentRecord

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  50. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  51. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  52. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

Ungrouped