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(referenceName: CharSequence, referenceId: Integer, start: Long, mapq: Integer, readName: CharSequence, sequence: CharSequence, mateReference: CharSequence, mateAlignmentStart: Long, cigar: CharSequence, qual: CharSequence, recordGroupName: CharSequence, recordGroupId: 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, attributes: CharSequence, recordGroupSequencingCenter: CharSequence, recordGroupDescription: CharSequence, recordGroupRunDateEpoch: Long, recordGroupFlowOrder: CharSequence, recordGroupKeySequence: CharSequence, recordGroupLibrary: CharSequence, recordGroupPredictedMedianInsertSize: Integer, recordGroupPlatform: CharSequence, recordGroupPlatformUnit: CharSequence, recordGroupSample: CharSequence, mateReferenceId: Integer, referenceLength: Long, referenceUrl: CharSequence, mateReferenceLength: Long, mateReferenceUrl: CharSequence, origQual: CharSequence)

  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 getCigar(): CharSequence

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

    Definition Classes
    AnyRef → Any

  16. def getDuplicateRead(): Boolean

  17. def getFailedVendorQualityChecks(): Boolean

  18. def getFirstOfPair(): Boolean

  19. def getMapq(): Integer

  20. def getMateAlignmentStart(): Long

  21. def getMateMapped(): Boolean

  22. def getMateNegativeStrand(): Boolean

  23. def getMateReference(): CharSequence

  24. def getMateReferenceId(): Integer

  25. def getMateReferenceLength(): Long

  26. def getMateReferenceUrl(): CharSequence

  27. def getMismatchingPositions(): CharSequence

  28. def getOrigQual(): CharSequence

  29. def getPrimaryAlignment(): Boolean

  30. def getProperPair(): Boolean

  31. def getQual(): CharSequence

  32. def getReadMapped(): Boolean

  33. def getReadName(): CharSequence

  34. def getReadNegativeStrand(): Boolean

  35. def getReadPaired(): Boolean

  36. def getRecordGroupDescription(): CharSequence

  37. def getRecordGroupFlowOrder(): CharSequence

  38. def getRecordGroupId(): Integer

  39. def getRecordGroupKeySequence(): CharSequence

  40. def getRecordGroupLibrary(): CharSequence

  41. def getRecordGroupName(): CharSequence

  42. def getRecordGroupPlatform(): CharSequence

  43. def getRecordGroupPlatformUnit(): CharSequence

  44. def getRecordGroupPredictedMedianInsertSize(): Integer

  45. def getRecordGroupRunDateEpoch(): Long

  46. def getRecordGroupSample(): CharSequence

  47. def getRecordGroupSequencingCenter(): CharSequence

  48. def getReferenceId(): Integer

  49. def getReferenceLength(): Long

  50. def getReferenceName(): CharSequence

  51. def getReferenceUrl(): CharSequence

  52. def getSchema(): Schema

    Definition Classes
    ADAMRecord → SpecificRecordBase → GenericContainer

  53. def getSecondOfPair(): Boolean

  54. def getSequence(): CharSequence

  55. def getStart(): Long

  56. def hashCode(): Int

    Definition Classes
    SpecificRecordBase → AnyRef → Any

  57. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  59. final def notify(): Unit

    Definition Classes
    AnyRef

  60. final def notifyAll(): Unit

    Definition Classes
    AnyRef

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

    Definition Classes
    ADAMRecord → SpecificRecordBase → IndexedRecord

  62. def setAttributes(value: CharSequence): Unit

  63. def setCigar(value: CharSequence): 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 setMateMapped(value: Boolean): Unit

  70. def setMateNegativeStrand(value: Boolean): Unit

  71. def setMateReference(value: CharSequence): Unit

  72. def setMateReferenceId(value: Integer): Unit

  73. def setMateReferenceLength(value: Long): Unit

  74. def setMateReferenceUrl(value: CharSequence): Unit

  75. def setMismatchingPositions(value: CharSequence): Unit

  76. def setOrigQual(value: CharSequence): Unit

  77. def setPrimaryAlignment(value: Boolean): Unit

  78. def setProperPair(value: Boolean): Unit

  79. def setQual(value: CharSequence): Unit

  80. def setReadMapped(value: Boolean): Unit

  81. def setReadName(value: CharSequence): Unit

  82. def setReadNegativeStrand(value: Boolean): Unit

  83. def setReadPaired(value: Boolean): Unit

  84. def setRecordGroupDescription(value: CharSequence): Unit

  85. def setRecordGroupFlowOrder(value: CharSequence): Unit

  86. def setRecordGroupId(value: Integer): Unit

  87. def setRecordGroupKeySequence(value: CharSequence): Unit

  88. def setRecordGroupLibrary(value: CharSequence): Unit

  89. def setRecordGroupName(value: CharSequence): Unit

  90. def setRecordGroupPlatform(value: CharSequence): Unit

  91. def setRecordGroupPlatformUnit(value: CharSequence): Unit

  92. def setRecordGroupPredictedMedianInsertSize(value: Integer): Unit

  93. def setRecordGroupRunDateEpoch(value: Long): Unit

  94. def setRecordGroupSample(value: CharSequence): Unit

  95. def setRecordGroupSequencingCenter(value: CharSequence): Unit

  96. def setReferenceId(value: Integer): Unit

  97. def setReferenceLength(value: Long): Unit

  98. def setReferenceName(value: CharSequence): Unit

  99. def setReferenceUrl(value: CharSequence): Unit

  100. def setSecondOfPair(value: Boolean): Unit

  101. def setSequence(value: CharSequence): Unit

  102. def setStart(value: Long): Unit

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

    Definition Classes
    AnyRef

  104. def toString(): String

    Definition Classes
    SpecificRecordBase → AnyRef → Any

  105. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  107. 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