class
AlignmentRecord extends Product
Instance Constructors
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new
AlignmentRecord(readInFragment: Option[Int], contigName: Option[String], start: Option[Long], oldPosition: Option[Long], end: Option[Long], mapq: Option[Int], readName: Option[String], sequence: Option[String], qual: Option[String], cigar: Option[String], oldCigar: Option[String], basesTrimmedFromStart: Option[Int], basesTrimmedFromEnd: Option[Int], readPaired: Option[Boolean], properPair: Option[Boolean], readMapped: Option[Boolean], mateMapped: Option[Boolean], failedVendorQualityChecks: Option[Boolean], duplicateRead: Option[Boolean], readNegativeStrand: Option[Boolean], mateNegativeStrand: Option[Boolean], primaryAlignment: Option[Boolean], secondaryAlignment: Option[Boolean], supplementaryAlignment: Option[Boolean], mismatchingPositions: Option[String], origQual: Option[String], attributes: Option[String], recordGroupName: Option[String], recordGroupSample: Option[String], mateAlignmentStart: Option[Long], mateContigName: Option[String], inferredInsertSize: Option[Long])
Value Members
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final
def
!=(arg0: AnyRef): Boolean
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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final
def
==(arg0: AnyRef): Boolean
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final
def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
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val
attributes: Option[String]
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val
basesTrimmedFromEnd: Option[Int]
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val
basesTrimmedFromStart: Option[Int]
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def
canEqual(that: Any): Boolean
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val
cigar: Option[String]
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def
clone(): AnyRef
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val
contigName: Option[String]
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val
duplicateRead: Option[Boolean]
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val
end: Option[Long]
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final
def
eq(arg0: AnyRef): Boolean
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def
equals(arg0: Any): Boolean
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val
failedVendorQualityChecks: Option[Boolean]
-
def
finalize(): Unit
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final
def
getClass(): Class[_]
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def
hashCode(): Int
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val
inferredInsertSize: Option[Long]
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final
def
isInstanceOf[T0]: Boolean
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val
mapq: Option[Int]
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val
mateAlignmentStart: Option[Long]
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val
mateContigName: Option[String]
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val
mateMapped: Option[Boolean]
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val
mateNegativeStrand: Option[Boolean]
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val
mismatchingPositions: Option[String]
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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val
oldCigar: Option[String]
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val
oldPosition: Option[Long]
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val
origQual: Option[String]
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val
primaryAlignment: Option[Boolean]
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def
productArity: Int
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def
productElement(i: Int): Any
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def
productIterator: Iterator[Any]
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def
productPrefix: String
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val
properPair: Option[Boolean]
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val
qual: Option[String]
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val
readInFragment: Option[Int]
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val
readMapped: Option[Boolean]
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val
readName: Option[String]
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val
readNegativeStrand: Option[Boolean]
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val
readPaired: Option[Boolean]
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val
recordGroupName: Option[String]
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val
recordGroupSample: Option[String]
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val
secondaryAlignment: Option[Boolean]
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val
sequence: Option[String]
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val
start: Option[Long]
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val
supplementaryAlignment: Option[Boolean]
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
toAvro: formats.avro.AlignmentRecord
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def
toString(): String
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
Inherited from Product
Inherited from Equals
Inherited from AnyRef
Inherited from Any