trait SamRecord extends AnyRef

A trait that fgbio uses as a replacement for SAMRecord. The trait is self-typed as a SamRecordIntermediate which is a sub-class of SAMRecord. It is done this wasy so that a) we can access superclass methods via SamRecordIntermediate but that self-typing here instead of extending hides the SAMRecord API from users of the class. The result is always a SAMRecord but isn't seen as such without casting.

Self Type
SamRecord with SamRecordIntermediate
Linear Supertypes
AnyRef, Any
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Inherited
  1. SamRecord
  2. AnyRef
  3. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from SamRecord to any2stringadd[SamRecord] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (SamRecord, B)
    Implicit
    This member is added by an implicit conversion from SamRecord to ArrowAssoc[SamRecord] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. final def apply[A](name: String): A
    Annotations
    @inline()
  7. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  8. def asSam: SAMRecord

    Returns this record as a SAMRecord.

  9. final def attributes: Map[String, Any]
    Annotations
    @inline()
  10. final def bases: Array[Byte]
    Annotations
    @inline()
  11. final def basesString: String
    Annotations
    @inline()
  12. final def bases_=(bs: String): Unit
    Annotations
    @inline()
  13. final def bases_=(bs: Array[Byte]): Unit
    Annotations
    @inline()
  14. final def cigar: Cigar
    Annotations
    @inline()
  15. final def cigarChanged(cigar: String): Unit
    Annotations
    @inline()
  16. final def cigar_=(cig: Cigar): Unit
    Annotations
    @inline()
  17. final def cigar_=(cig: String): Unit
    Annotations
    @inline()
  18. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  19. final def duplicate: Boolean
    Annotations
    @inline()
  20. final def duplicate_=(dupe: Boolean): Unit
    Annotations
    @inline()
  21. final def end: Int
    Annotations
    @inline()
  22. def ensuring(cond: (SamRecord) ⇒ Boolean, msg: ⇒ Any): SamRecord
    Implicit
    This member is added by an implicit conversion from SamRecord to Ensuring[SamRecord] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  23. def ensuring(cond: (SamRecord) ⇒ Boolean): SamRecord
    Implicit
    This member is added by an implicit conversion from SamRecord to Ensuring[SamRecord] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  24. def ensuring(cond: Boolean, msg: ⇒ Any): SamRecord
    Implicit
    This member is added by an implicit conversion from SamRecord to Ensuring[SamRecord] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  25. def ensuring(cond: Boolean): SamRecord
    Implicit
    This member is added by an implicit conversion from SamRecord to Ensuring[SamRecord] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  26. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  27. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  28. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  29. final def firstOfPair: Boolean
    Annotations
    @inline()
  30. final def firstOfPair_=(first: Boolean): Unit
    Annotations
    @inline()
  31. final def flags: Int
    Annotations
    @inline()
  32. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from SamRecord to StringFormat[SamRecord] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  33. final def get[A](name: String): Option[A]
    Annotations
    @inline()
  34. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  35. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  36. final def header: SAMFileHeader
    Annotations
    @inline()
  37. final def header_=(header: SAMFileHeader): Unit
    Annotations
    @inline()
  38. def id: String

    Returns a string that is useful to identify a SamRecord, mostly for testing and error messages.

  39. final def insertSize: Int
    Annotations
    @inline()
  40. final def insertSize_=(s: Int): Unit
    Annotations
    @inline()
  41. def isFrPair: Boolean

    Returns true if the read is mapped in an FR pair, false otherwise.

  42. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  43. final def length: Int
    Annotations
    @inline()
  44. final def mapped: Boolean
    Annotations
    @inline()
  45. final def mapped_=(mapped: Boolean): Unit
    Annotations
    @inline()
  46. final def mapq: Int
    Annotations
    @inline()
  47. final def mapq_=(q: Int): Unit
    Annotations
    @inline()
  48. final def mateEnd: Option[Int]
    Annotations
    @inline()
  49. final def mateMapped: Boolean
    Annotations
    @inline()
  50. final def mateMapped_=(mapped: Boolean): Unit
    Annotations
    @inline()
  51. final def mateNegativeStrand: Boolean
    Annotations
    @inline()
  52. final def mateNegativeStrand_=(negative: Boolean): Unit
    Annotations
    @inline()
  53. final def matePositiveStrand: Boolean
    Annotations
    @inline()
  54. final def matePositiveStrand_=(positive: Boolean): Unit
    Annotations
    @inline()
  55. final def mateRefIndex: Int
    Annotations
    @inline()
  56. final def mateRefIndex_=(index: Int): Unit
    Annotations
    @inline()
  57. final def mateRefName: String
    Annotations
    @inline()
  58. final def mateRefName_=(name: String): Unit
    Annotations
    @inline()
  59. final def mateStart: Int
    Annotations
    @inline()
  60. final def mateStart_=(s: Int): Unit
    Annotations
    @inline()
  61. final def mateUnmapped: Boolean
    Annotations
    @inline()
  62. final def mateUnmapped_=(unmapped: Boolean): Unit
    Annotations
    @inline()
  63. final def name: String
    Annotations
    @inline()
  64. final def name_=(name: String): Unit
    Annotations
    @inline()
  65. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  66. final def negativeStrand: Boolean
    Annotations
    @inline()
  67. final def negativeStrand_=(negative: Boolean): Unit
    Annotations
    @inline()
  68. final def notify(): Unit
    Definition Classes
    AnyRef
  69. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  70. def pairOrientation: PairOrientation

    Gets the PairOrientation of the record.

  71. final def paired: Boolean
    Annotations
    @inline()
  72. final def paired_=(paired: Boolean): Unit
    Annotations
    @inline()
  73. final def pf: Boolean
    Annotations
    @inline()
  74. final def pf_=(pf: Boolean): Unit
    Annotations
    @inline()
  75. final def positiveStrand: Boolean
    Annotations
    @inline()
  76. final def positiveStrand_=(positive: Boolean): Unit
    Annotations
    @inline()
  77. final def properlyPaired: Boolean
    Annotations
    @inline()
  78. final def properlyPaired_=(paired: Boolean): Unit
    Annotations
    @inline()
  79. final def quals: Array[Byte]
    Annotations
    @inline()
  80. final def qualsString: String
    Annotations
    @inline()
  81. final def quals_=(qs: String): Unit
    Annotations
    @inline()
  82. final def quals_=(qs: Array[Byte]): Unit
    Annotations
    @inline()
  83. final def readGroup: SAMReadGroupRecord
    Annotations
    @inline()
  84. final def readPosAtRefPos(pos: Int, returnLastBaseIfDeleted: Boolean): Int
    Annotations
    @inline()
  85. final def refIndex: Int
    Annotations
    @inline()
  86. final def refIndex_=(index: Int): Unit
    Annotations
    @inline()
  87. final def refName: String
    Annotations
    @inline()
  88. final def refName_=(name: String): Unit
    Annotations
    @inline()
  89. final def refPosAtReadPos(pos: Int): Int
    Annotations
    @inline()
  90. final def secondOfPair: Boolean
    Annotations
    @inline()
  91. final def secondOfPair_=(second: Boolean): Unit
    Annotations
    @inline()
  92. final def secondary: Boolean
    Annotations
    @inline()
  93. final def secondary_=(secondary: Boolean): Unit
    Annotations
    @inline()
  94. final def start: Int
    Annotations
    @inline()
  95. final def start_=(s: Int): Unit
    Annotations
    @inline()
  96. final def supplementary: Boolean
    Annotations
    @inline()
  97. final def supplementary_=(supplementary: Boolean): Unit
    Annotations
    @inline()
  98. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  99. def toString(): String
    Definition Classes
    AnyRef → Any
  100. final def transientAttrs: TransientAttrs
    Annotations
    @inline()
  101. final def unclippedEnd: Int
    Annotations
    @inline()
  102. final def unclippedStart: Int
    Annotations
    @inline()
  103. final def unmapped: Boolean
    Annotations
    @inline()
  104. final def unmapped_=(unmapped: Boolean): Unit
    Annotations
    @inline()
  105. final def update(name: String, value: Any): Unit
    Annotations
    @inline()
  106. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  107. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  108. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  109. def →[B](y: B): (SamRecord, B)
    Implicit
    This member is added by an implicit conversion from SamRecord to ArrowAssoc[SamRecord] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from SamRecord to any2stringadd[SamRecord]

Inherited by implicit conversion StringFormat from SamRecord to StringFormat[SamRecord]

Inherited by implicit conversion Ensuring from SamRecord to Ensuring[SamRecord]

Inherited by implicit conversion ArrowAssoc from SamRecord to ArrowAssoc[SamRecord]

Ungrouped