org.bdgenomics.adam.avro

ADAMPileup

class ADAMPileup extends SpecificRecordBase with SpecificRecord

Linear Supertypes
SpecificRecordBase, Comparable[SpecificRecord], SpecificRecord, IndexedRecord, GenericContainer, AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. ADAMPileup
  2. SpecificRecordBase
  3. Comparable
  4. SpecificRecord
  5. IndexedRecord
  6. GenericContainer
  7. AnyRef
  8. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Instance Constructors

  1. new ADAMPileup(contig: ADAMContig, position: Long, rangeOffset: Integer, rangeLength: Integer, referenceBase: Base, readBase: Base, sangerQuality: Integer, mapQuality: Integer, numSoftClipped: Integer, numReverseStrand: Integer, countAtPosition: Integer, readName: CharSequence, readStart: Long, readEnd: Long, recordGroupSequencingCenter: CharSequence, recordGroupDescription: CharSequence, recordGroupRunDateEpoch: Long, recordGroupFlowOrder: CharSequence, recordGroupKeySequence: CharSequence, recordGroupLibrary: CharSequence, recordGroupPredictedMedianInsertSize: Integer, recordGroupPlatform: CharSequence, recordGroupPlatformUnit: CharSequence, recordGroupSample: CharSequence)

  2. new ADAMPileup()

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. def clone(): AnyRef

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

  8. def compareTo(arg0: SpecificRecord): Int

    Definition Classes
    SpecificRecordBase → Comparable

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

    Definition Classes
    AnyRef

  10. def equals(arg0: Any): Boolean

    Definition Classes
    SpecificRecordBase → AnyRef → Any

  11. def finalize(): Unit

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

  12. def get(arg0: Int): AnyRef

    Definition Classes
    ADAMPileup → SpecificRecordBase → IndexedRecord

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

    Definition Classes
    AnyRef → Any

  14. def getContig(): ADAMContig

  15. def getCountAtPosition(): Integer

  16. def getMapQuality(): Integer

  17. def getNumReverseStrand(): Integer

  18. def getNumSoftClipped(): Integer

  19. def getPosition(): Long

  20. def getRangeLength(): Integer

  21. def getRangeOffset(): Integer

  22. def getReadBase(): Base

  23. def getReadEnd(): Long

  24. def getReadName(): CharSequence

  25. def getReadStart(): Long

  26. def getRecordGroupDescription(): CharSequence

  27. def getRecordGroupFlowOrder(): CharSequence

  28. def getRecordGroupKeySequence(): CharSequence

  29. def getRecordGroupLibrary(): CharSequence

  30. def getRecordGroupPlatform(): CharSequence

  31. def getRecordGroupPlatformUnit(): CharSequence

  32. def getRecordGroupPredictedMedianInsertSize(): Integer

  33. def getRecordGroupRunDateEpoch(): Long

  34. def getRecordGroupSample(): CharSequence

  35. def getRecordGroupSequencingCenter(): CharSequence

  36. def getReferenceBase(): Base

  37. def getSangerQuality(): Integer

  38. def getSchema(): Schema

    Definition Classes
    ADAMPileup → SpecificRecordBase → GenericContainer

  39. def hashCode(): Int

    Definition Classes
    SpecificRecordBase → AnyRef → Any

  40. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  42. final def notify(): Unit

    Definition Classes
    AnyRef

  43. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  44. def put(arg0: Int, arg1: Any): Unit

    Definition Classes
    ADAMPileup → SpecificRecordBase → IndexedRecord

  45. def setContig(value: ADAMContig): Unit

  46. def setCountAtPosition(value: Integer): Unit

  47. def setMapQuality(value: Integer): Unit

  48. def setNumReverseStrand(value: Integer): Unit

  49. def setNumSoftClipped(value: Integer): Unit

  50. def setPosition(value: Long): Unit

  51. def setRangeLength(value: Integer): Unit

  52. def setRangeOffset(value: Integer): Unit

  53. def setReadBase(value: Base): Unit

  54. def setReadEnd(value: Long): Unit

  55. def setReadName(value: CharSequence): Unit

  56. def setReadStart(value: Long): Unit

  57. def setRecordGroupDescription(value: CharSequence): Unit

  58. def setRecordGroupFlowOrder(value: CharSequence): Unit

  59. def setRecordGroupKeySequence(value: CharSequence): Unit

  60. def setRecordGroupLibrary(value: CharSequence): Unit

  61. def setRecordGroupPlatform(value: CharSequence): Unit

  62. def setRecordGroupPlatformUnit(value: CharSequence): Unit

  63. def setRecordGroupPredictedMedianInsertSize(value: Integer): Unit

  64. def setRecordGroupRunDateEpoch(value: Long): Unit

  65. def setRecordGroupSample(value: CharSequence): Unit

  66. def setRecordGroupSequencingCenter(value: CharSequence): Unit

  67. def setReferenceBase(value: Base): Unit

  68. def setSangerQuality(value: Integer): Unit

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

    Definition Classes
    AnyRef

  70. def toString(): String

    Definition Classes
    SpecificRecordBase → AnyRef → Any

  71. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from SpecificRecordBase

Inherited from Comparable[SpecificRecord]

Inherited from SpecificRecord

Inherited from IndexedRecord

Inherited from GenericContainer

Inherited from AnyRef

Inherited from Any

Ungrouped