org.bdgenomics.adam.sql

AlignmentRecord

class AlignmentRecord extends Product

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Product, Equals, AnyRef, Any
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  2. Product
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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])

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. val attributes: Option[String]

  8. val basesTrimmedFromEnd: Option[Int]

  9. val basesTrimmedFromStart: Option[Int]

  10. def canEqual(that: Any): Boolean

    Definition Classes
    AlignmentRecord → Equals

  11. val cigar: Option[String]

  12. def clone(): AnyRef

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

  13. val contigName: Option[String]

  14. val duplicateRead: Option[Boolean]

  15. val end: Option[Long]

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

    Definition Classes
    AnyRef

  17. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  18. val failedVendorQualityChecks: Option[Boolean]

  19. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  21. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  22. val inferredInsertSize: Option[Long]

  23. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  24. val mapq: Option[Int]

  25. val mateAlignmentStart: Option[Long]

  26. val mateContigName: Option[String]

  27. val mateMapped: Option[Boolean]

  28. val mateNegativeStrand: Option[Boolean]

  29. val mismatchingPositions: Option[String]

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

    Definition Classes
    AnyRef

  31. final def notify(): Unit

    Definition Classes
    AnyRef

  32. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  33. val oldCigar: Option[String]

  34. val oldPosition: Option[Long]

  35. val origQual: Option[String]

  36. val primaryAlignment: Option[Boolean]

  37. def productArity: Int

    Definition Classes
    AlignmentRecord → Product

  38. def productElement(i: Int): Any

    Definition Classes
    AlignmentRecord → Product

  39. def productIterator: Iterator[Any]

    Definition Classes
    Product

  40. def productPrefix: String

    Definition Classes
    Product

  41. val properPair: Option[Boolean]

  42. val qual: Option[String]

  43. val readInFragment: Option[Int]

  44. val readMapped: Option[Boolean]

  45. val readName: Option[String]

  46. val readNegativeStrand: Option[Boolean]

  47. val readPaired: Option[Boolean]

  48. val recordGroupName: Option[String]

  49. val recordGroupSample: Option[String]

  50. val secondaryAlignment: Option[Boolean]

  51. val sequence: Option[String]

  52. val start: Option[Long]

  53. val supplementaryAlignment: Option[Boolean]

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

    Definition Classes
    AnyRef

  55. def toAvro: formats.avro.AlignmentRecord

  56. def toString(): String

    Definition Classes
    AnyRef → Any

  57. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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