Class/Object

org.bdgenomics.adam.sql

AlignmentRecord

Related Docs: object AlignmentRecord | package sql

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case class AlignmentRecord(readInFragment: Option[Int] = None, contigName: Option[String] = None, start: Option[Long] = None, oldPosition: Option[Long] = None, end: Option[Long] = None, mapq: Option[Int] = None, readName: Option[String] = None, sequence: Option[String] = None, qual: Option[String] = None, cigar: Option[String] = None, oldCigar: 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, origQual: Option[String] = None, attributes: Option[String] = None, recordGroupName: Option[String] = None, recordGroupSample: Option[String] = None, mateAlignmentStart: Option[Long] = None, mateContigName: Option[String] = None, inferredInsertSize: Option[Long] = 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(readInFragment: Option[Int] = None, contigName: Option[String] = None, start: Option[Long] = None, oldPosition: Option[Long] = None, end: Option[Long] = None, mapq: Option[Int] = None, readName: Option[String] = None, sequence: Option[String] = None, qual: Option[String] = None, cigar: Option[String] = None, oldCigar: 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, origQual: Option[String] = None, attributes: Option[String] = None, recordGroupName: Option[String] = None, recordGroupSample: Option[String] = None, mateAlignmentStart: Option[Long] = None, mateContigName: Option[String] = None, inferredInsertSize: Option[Long] = 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 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. val failedVendorQualityChecks: Option[Boolean]

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  16. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  17. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  18. val inferredInsertSize: Option[Long]

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  19. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  20. val mapq: Option[Int]

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  21. val mateAlignmentStart: Option[Long]

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  22. val mateContigName: Option[String]

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  23. val mateMapped: Option[Boolean]

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  24. val mateNegativeStrand: Option[Boolean]

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  25. val mismatchingPositions: Option[String]

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

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    Definition Classes
    AnyRef
  27. final def notify(): Unit

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    Definition Classes
    AnyRef
  28. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  29. val oldCigar: Option[String]

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  30. val oldPosition: Option[Long]

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  31. val origQual: Option[String]

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  32. val primaryAlignment: Option[Boolean]

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  33. def productArity: Int

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    Definition Classes
    AlignmentRecord → Product
  34. def productElement(i: Int): Any

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    Definition Classes
    AlignmentRecord → Product
  35. val properPair: Option[Boolean]

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  36. val qual: Option[String]

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  37. val readInFragment: Option[Int]

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  38. val readMapped: Option[Boolean]

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  39. val readName: Option[String]

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  40. val readNegativeStrand: Option[Boolean]

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  41. val readPaired: Option[Boolean]

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  42. val recordGroupName: Option[String]

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  43. val recordGroupSample: 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