org.bdgenomics.adam.avro

ADAMRecord

class ADAMRecord extends SpecificRecordBase with SpecificRecord

Linear Supertypes
SpecificRecordBase, Comparable[SpecificRecord], SpecificRecord, IndexedRecord, GenericContainer, AnyRef, Any
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Inherited
  1. ADAMRecord
  2. SpecificRecordBase
  3. Comparable
  4. SpecificRecord
  5. IndexedRecord
  6. GenericContainer
  7. AnyRef
  8. Any
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Visibility
  1. Public
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Instance Constructors

  1. new ADAMRecord(contig: ADAMContig, start: Long, mapq: Integer, readName: CharSequence, sequence: CharSequence, mateReference: CharSequence, mateAlignmentStart: Long, cigar: CharSequence, qual: CharSequence, recordGroupName: CharSequence, recordGroupId: Integer, basesTrimmedFromStart: Integer, basesTrimmedFromEnd: Integer, readPaired: Boolean, properPair: Boolean, readMapped: Boolean, mateMapped: Boolean, readNegativeStrand: Boolean, mateNegativeStrand: Boolean, firstOfPair: Boolean, secondOfPair: Boolean, primaryAlignment: Boolean, failedVendorQualityChecks: Boolean, duplicateRead: Boolean, mismatchingPositions: CharSequence, origQual: CharSequence, attributes: CharSequence, recordGroupSequencingCenter: CharSequence, recordGroupDescription: CharSequence, recordGroupRunDateEpoch: Long, recordGroupFlowOrder: CharSequence, recordGroupKeySequence: CharSequence, recordGroupLibrary: CharSequence, recordGroupPredictedMedianInsertSize: Integer, recordGroupPlatform: CharSequence, recordGroupPlatformUnit: CharSequence, recordGroupSample: CharSequence, mateContig: ADAMContig)

  2. new ADAMRecord()

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
    ADAMRecord → SpecificRecordBase → IndexedRecord

  13. def getAttributes(): CharSequence

  14. def getBasesTrimmedFromEnd(): Integer

  15. def getBasesTrimmedFromStart(): Integer

  16. def getCigar(): CharSequence

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

    Definition Classes
    AnyRef → Any

  18. def getContig(): ADAMContig

  19. def getDuplicateRead(): Boolean

  20. def getFailedVendorQualityChecks(): Boolean

  21. def getFirstOfPair(): Boolean

  22. def getMapq(): Integer

  23. def getMateAlignmentStart(): Long

  24. def getMateContig(): ADAMContig

  25. def getMateMapped(): Boolean

  26. def getMateNegativeStrand(): Boolean

  27. def getMateReference(): CharSequence

  28. def getMismatchingPositions(): CharSequence

  29. def getOrigQual(): CharSequence

  30. def getPrimaryAlignment(): Boolean

  31. def getProperPair(): Boolean

  32. def getQual(): CharSequence

  33. def getReadMapped(): Boolean

  34. def getReadName(): CharSequence

  35. def getReadNegativeStrand(): Boolean

  36. def getReadPaired(): Boolean

  37. def getRecordGroupDescription(): CharSequence

  38. def getRecordGroupFlowOrder(): CharSequence

  39. def getRecordGroupId(): Integer

  40. def getRecordGroupKeySequence(): CharSequence

  41. def getRecordGroupLibrary(): CharSequence

  42. def getRecordGroupName(): CharSequence

  43. def getRecordGroupPlatform(): CharSequence

  44. def getRecordGroupPlatformUnit(): CharSequence

  45. def getRecordGroupPredictedMedianInsertSize(): Integer

  46. def getRecordGroupRunDateEpoch(): Long

  47. def getRecordGroupSample(): CharSequence

  48. def getRecordGroupSequencingCenter(): CharSequence

  49. def getSchema(): Schema

    Definition Classes
    ADAMRecord → SpecificRecordBase → GenericContainer

  50. def getSecondOfPair(): Boolean

  51. def getSequence(): CharSequence

  52. def getStart(): Long

  53. def hashCode(): Int

    Definition Classes
    SpecificRecordBase → AnyRef → Any

  54. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  56. final def notify(): Unit

    Definition Classes
    AnyRef

  57. final def notifyAll(): Unit

    Definition Classes
    AnyRef

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

    Definition Classes
    ADAMRecord → SpecificRecordBase → IndexedRecord

  59. def setAttributes(value: CharSequence): Unit

  60. def setBasesTrimmedFromEnd(value: Integer): Unit

  61. def setBasesTrimmedFromStart(value: Integer): Unit

  62. def setCigar(value: CharSequence): Unit

  63. def setContig(value: ADAMContig): Unit

  64. def setDuplicateRead(value: Boolean): Unit

  65. def setFailedVendorQualityChecks(value: Boolean): Unit

  66. def setFirstOfPair(value: Boolean): Unit

  67. def setMapq(value: Integer): Unit

  68. def setMateAlignmentStart(value: Long): Unit

  69. def setMateContig(value: ADAMContig): Unit

  70. def setMateMapped(value: Boolean): Unit

  71. def setMateNegativeStrand(value: Boolean): Unit

  72. def setMateReference(value: CharSequence): Unit

  73. def setMismatchingPositions(value: CharSequence): Unit

  74. def setOrigQual(value: CharSequence): Unit

  75. def setPrimaryAlignment(value: Boolean): Unit

  76. def setProperPair(value: Boolean): Unit

  77. def setQual(value: CharSequence): Unit

  78. def setReadMapped(value: Boolean): Unit

  79. def setReadName(value: CharSequence): Unit

  80. def setReadNegativeStrand(value: Boolean): Unit

  81. def setReadPaired(value: Boolean): Unit

  82. def setRecordGroupDescription(value: CharSequence): Unit

  83. def setRecordGroupFlowOrder(value: CharSequence): Unit

  84. def setRecordGroupId(value: Integer): Unit

  85. def setRecordGroupKeySequence(value: CharSequence): Unit

  86. def setRecordGroupLibrary(value: CharSequence): Unit

  87. def setRecordGroupName(value: CharSequence): Unit

  88. def setRecordGroupPlatform(value: CharSequence): Unit

  89. def setRecordGroupPlatformUnit(value: CharSequence): Unit

  90. def setRecordGroupPredictedMedianInsertSize(value: Integer): Unit

  91. def setRecordGroupRunDateEpoch(value: Long): Unit

  92. def setRecordGroupSample(value: CharSequence): Unit

  93. def setRecordGroupSequencingCenter(value: CharSequence): Unit

  94. def setSecondOfPair(value: Boolean): Unit

  95. def setSequence(value: CharSequence): Unit

  96. def setStart(value: Long): Unit

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

    Definition Classes
    AnyRef

  98. def toString(): String

    Definition Classes
    SpecificRecordBase → AnyRef → Any

  99. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  101. 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