Class/Object

org.bdgenomics.adam.sql

AlignmentRecord

Related Docs: object AlignmentRecord | package sql

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class AlignmentRecord extends Product

Linear Supertypes
Product, Equals, AnyRef, Any
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Inherited
  1. AlignmentRecord
  2. Product
  3. Equals
  4. AnyRef
  5. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new AlignmentRecord(readInFragment: Option[Int], contigName: Option[String], start: Option[Long], oldPosition: Option[Long], end: Option[Long], mapq: Option[Int], readName: Option[String], sequence: Option[String], qual: Option[String], cigar: Option[String], oldCigar: Option[String], basesTrimmedFromStart: Option[Int], basesTrimmedFromEnd: Option[Int], readPaired: Option[Boolean], properPair: Option[Boolean], readMapped: Option[Boolean], mateMapped: Option[Boolean], failedVendorQualityChecks: Option[Boolean], duplicateRead: Option[Boolean], readNegativeStrand: Option[Boolean], mateNegativeStrand: Option[Boolean], primaryAlignment: Option[Boolean], secondaryAlignment: Option[Boolean], supplementaryAlignment: Option[Boolean], mismatchingPositions: Option[String], origQual: Option[String], attributes: Option[String], recordGroupName: Option[String], recordGroupSample: Option[String], mateAlignmentStart: Option[Long], mateContigName: Option[String], inferredInsertSize: Option[Long])

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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 contigName: Option[String]

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  12. val duplicateRead: Option[Boolean]

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  13. val end: Option[Long]

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

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    Definition Classes
    AnyRef

  15. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  16. val failedVendorQualityChecks: Option[Boolean]

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  17. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  19. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  20. val inferredInsertSize: Option[Long]

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  21. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  22. val mapq: Option[Int]

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  23. val mateAlignmentStart: Option[Long]

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  24. val mateContigName: Option[String]

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  25. val mateMapped: Option[Boolean]

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  26. val mateNegativeStrand: Option[Boolean]

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  27. val mismatchingPositions: Option[String]

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

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    Definition Classes
    AnyRef

  29. final def notify(): Unit

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    Definition Classes
    AnyRef

  30. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  31. val oldCigar: Option[String]

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  32. val oldPosition: Option[Long]

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  33. val origQual: Option[String]

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  34. val primaryAlignment: Option[Boolean]

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  35. def productArity: Int

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    Definition Classes
    AlignmentRecord → Product

  36. def productElement(i: Int): Any

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    Definition Classes
    AlignmentRecord → Product

  37. def productIterator: Iterator[Any]

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    Definition Classes
    Product

  38. def productPrefix: String

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    Definition Classes
    Product

  39. val properPair: Option[Boolean]

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  40. val qual: Option[String]

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  41. val readInFragment: Option[Int]

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  42. val readMapped: Option[Boolean]

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  43. val readName: Option[String]

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  44. val readNegativeStrand: Option[Boolean]

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  45. val readPaired: Option[Boolean]

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  46. val recordGroupName: Option[String]

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  47. val recordGroupSample: Option[String]

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  48. val secondaryAlignment: Option[Boolean]

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  49. val sequence: Option[String]

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  50. val start: Option[Long]

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  51. val supplementaryAlignment: Option[Boolean]

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

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    Definition Classes
    AnyRef

  53. def toAvro: formats.avro.AlignmentRecord

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  54. def toString(): String

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    Definition Classes
    AnyRef → Any

  55. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

Ungrouped