case class Alignment(referenceName: Option[String] = None, start: Option[Long] = None, originalStart: Option[Long] = None, end: Option[Long] = None, mappingQuality: Option[Int] = None, readName: Option[String] = None, sequence: Option[String] = None, qualityScores: Option[String] = None, cigar: Option[String] = None, originalCigar: Option[String] = None, basesTrimmedFromStart: Option[Int] = None, basesTrimmedFromEnd: Option[Int] = None, readPaired: Option[Boolean] = None, properPair: Option[Boolean] = None, readMapped: Option[Boolean] = None, mateMapped: Option[Boolean] = None, failedVendorQualityChecks: Option[Boolean] = None, duplicateRead: Option[Boolean] = None, readNegativeStrand: Option[Boolean] = None, mateNegativeStrand: Option[Boolean] = None, primaryAlignment: Option[Boolean] = None, secondaryAlignment: Option[Boolean] = None, supplementaryAlignment: Option[Boolean] = None, mismatchingPositions: Option[String] = None, originalQualityScores: Option[String] = None, readGroupId: Option[String] = None, readGroupSampleId: Option[String] = None, mateAlignmentStart: Option[Long] = None, mateReferenceName: Option[String] = None, insertSize: Option[Long] = None, readInFragment: Option[Int] = None, attributes: Option[String] = None) extends Product with Serializable
Linear Supertypes
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Inherited
- Alignment
- Serializable
- Serializable
- Product
- Equals
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- Any
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Visibility
- Public
- All
Instance Constructors
- new Alignment(referenceName: Option[String] = None, start: Option[Long] = None, originalStart: Option[Long] = None, end: Option[Long] = None, mappingQuality: Option[Int] = None, readName: Option[String] = None, sequence: Option[String] = None, qualityScores: Option[String] = None, cigar: Option[String] = None, originalCigar: Option[String] = None, basesTrimmedFromStart: Option[Int] = None, basesTrimmedFromEnd: Option[Int] = None, readPaired: Option[Boolean] = None, properPair: Option[Boolean] = None, readMapped: Option[Boolean] = None, mateMapped: Option[Boolean] = None, failedVendorQualityChecks: Option[Boolean] = None, duplicateRead: Option[Boolean] = None, readNegativeStrand: Option[Boolean] = None, mateNegativeStrand: Option[Boolean] = None, primaryAlignment: Option[Boolean] = None, secondaryAlignment: Option[Boolean] = None, supplementaryAlignment: Option[Boolean] = None, mismatchingPositions: Option[String] = None, originalQualityScores: Option[String] = None, readGroupId: Option[String] = None, readGroupSampleId: Option[String] = None, mateAlignmentStart: Option[Long] = None, mateReferenceName: Option[String] = None, insertSize: Option[Long] = None, readInFragment: Option[Int] = None, attributes: Option[String] = None)
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
- val attributes: Option[String]
- val basesTrimmedFromEnd: Option[Int]
- val basesTrimmedFromStart: Option[Int]
-
def
canEqual(that: Any): Boolean
- Definition Classes
- Alignment → Equals
- val cigar: Option[String]
-
def
clone(): AnyRef
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native() @HotSpotIntrinsicCandidate()
- val duplicateRead: Option[Boolean]
- val end: Option[Long]
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
- val failedVendorQualityChecks: Option[Boolean]
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
- Annotations
- @native() @HotSpotIntrinsicCandidate()
- val insertSize: Option[Long]
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
- val mappingQuality: Option[Int]
- val mateAlignmentStart: Option[Long]
- val mateMapped: Option[Boolean]
- val mateNegativeStrand: Option[Boolean]
- val mateReferenceName: Option[String]
- val mismatchingPositions: Option[String]
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
- val originalCigar: Option[String]
- val originalQualityScores: Option[String]
- val originalStart: Option[Long]
- val primaryAlignment: Option[Boolean]
-
def
productArity: Int
- Definition Classes
- Alignment → Product
-
def
productElement(i: Int): Any
- Definition Classes
- Alignment → Product
- val properPair: Option[Boolean]
- val qualityScores: Option[String]
- val readGroupId: Option[String]
- val readGroupSampleId: Option[String]
- val readInFragment: Option[Int]
- val readMapped: Option[Boolean]
- val readName: Option[String]
- val readNegativeStrand: Option[Boolean]
- val readPaired: Option[Boolean]
- val referenceName: Option[String]
- val secondaryAlignment: Option[Boolean]
- val sequence: Option[String]
- val start: Option[Long]
- val supplementaryAlignment: Option[Boolean]
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
- def toAvro: formats.avro.Alignment
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
Deprecated Value Members
-
def
finalize(): Unit
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
- Deprecated
(Since version ) see corresponding Javadoc for more information.