org.bdgenomics.adam.sql

# Alignment

###
Related Docs: object Alignment | package sql

#### 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
2. All

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

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. #### def finalize(): Unit

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

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

    Definition Classes
      AnyRef → Any

17. #### val insertSize: Option[Long]

18. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

19. #### val mappingQuality: Option[Int]

20. #### val mateAlignmentStart: Option[Long]

21. #### val mateMapped: Option[Boolean]

22. #### val mateNegativeStrand: Option[Boolean]

23. #### val mateReferenceName: Option[String]

24. #### val mismatchingPositions: Option[String]

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

    Definition Classes
      AnyRef

26. #### final def notify(): Unit

    Definition Classes
      AnyRef

27. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

28. #### val originalCigar: Option[String]

29. #### val originalQualityScores: Option[String]

30. #### val originalStart: Option[Long]

31. #### val primaryAlignment: Option[Boolean]

32. #### def productArity: Int

    Definition Classes
      Alignment → Product

33. #### def productElement(i: Int): Any

    Definition Classes
      Alignment → Product

34. #### val properPair: Option[Boolean]

35. #### val qualityScores: Option[String]

36. #### val readGroupId: Option[String]

37. #### val readGroupSampleId: Option[String]

38. #### val readInFragment: Option[Int]

39. #### val readMapped: Option[Boolean]

40. #### val readName: Option[String]

41. #### val readNegativeStrand: Option[Boolean]

42. #### val readPaired: Option[Boolean]

43. #### val referenceName: Option[String]

44. #### val secondaryAlignment: Option[Boolean]

45. #### val sequence: Option[String]

46. #### val start: Option[Long]

47. #### val supplementaryAlignment: Option[Boolean]

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

    Definition Classes
      AnyRef

49. #### def toAvro: formats.avro.Alignment

50. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from Serializable

### Inherited from Product

### Inherited from Equals

### Inherited from AnyRef

### Inherited from Any

### Ungrouped