class DemuxFastqs extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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Inherited
- DemuxFastqs
- LazyLogging
- FgBioTool
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Implicitly
- by any2stringadd
- by StringFormat
- by Ensuring
- by ArrowAssoc
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Visibility
- Public
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Instance Constructors
- new DemuxFastqs(inputs: Seq[commons.CommonsDef.PathToFastq], output: commons.CommonsDef.DirPath, metadata: commons.CommonsDef.FilePath, readStructures: Seq[ReadStructure], metrics: Option[commons.CommonsDef.FilePath] = None, columnForSampleBarcode: String = "Sample_Barcode", unmatched: String = ..., qualityFormat: Option[FastqQualityFormat] = None, threads: Int = 1, maxMismatches: Int = 1, minMismatchDelta: Int = 2, maxNoCalls: Int = 2, sortOrder: SortOrder = SortOrder.queryname, umiTag: String = ConsensusTags.UmiBases, platformUnit: Option[String] = None, sequencingCenter: Option[String] = None, predictedInsertSize: Option[Integer] = None, platformModel: Option[String] = None, comments: List[String] = Nil, runDate: Option[Iso8601Date] = None, outputFastqs: Boolean = false, illuminaStandards: Boolean = false)
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from DemuxFastqs to any2stringadd[DemuxFastqs] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
-
def
->[B](y: B): (DemuxFastqs, B)
- Implicit
- This member is added by an implicit conversion from DemuxFastqs to ArrowAssoc[DemuxFastqs] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
- Annotations
- @inline()
-
final
def
==(arg0: Any): Boolean
- Definition Classes
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-
final
def
asInstanceOf[T0]: T0
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-
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
- val columnForSampleBarcode: String
- val comments: List[String]
-
def
ensuring(cond: (DemuxFastqs) ⇒ Boolean, msg: ⇒ Any): DemuxFastqs
- Implicit
- This member is added by an implicit conversion from DemuxFastqs to Ensuring[DemuxFastqs] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (DemuxFastqs) ⇒ Boolean): DemuxFastqs
- Implicit
- This member is added by an implicit conversion from DemuxFastqs to Ensuring[DemuxFastqs] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): DemuxFastqs
- Implicit
- This member is added by an implicit conversion from DemuxFastqs to Ensuring[DemuxFastqs] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): DemuxFastqs
- Implicit
- This member is added by an implicit conversion from DemuxFastqs to Ensuring[DemuxFastqs] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
execute(): Unit
- Definition Classes
- DemuxFastqs → FgBioTool
-
def
fail(exit: Int, message: String): Nothing
Fail with a specific error code and message.
Fail with a specific error code and message.
- Definition Classes
- FgBioTool
-
def
fail(message: String): Nothing
Fail with the default exit code and a message.
Fail with the default exit code and a message.
- Definition Classes
- FgBioTool
-
def
fail(exit: Int): Nothing
Fail with just an exit code.
Fail with just an exit code.
- Definition Classes
- FgBioTool
-
def
finalize(): Unit
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
-
def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from DemuxFastqs to StringFormat[DemuxFastqs] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
- Annotations
- @inline()
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- val illuminaStandards: Boolean
- val inputs: Seq[commons.CommonsDef.PathToFastq]
-
def
invalid(message: String): Nothing
Generates a new validation exception with the given message.
Generates a new validation exception with the given message.
- Definition Classes
- FgBioTool
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
lazy val
logger: Logger
- Attributes
- protected
- Definition Classes
- LazyLogging
- val maxMismatches: Int
- val maxNoCalls: Int
- val metadata: commons.CommonsDef.FilePath
- val metrics: Option[commons.CommonsDef.FilePath]
- val minMismatchDelta: Int
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- val output: commons.CommonsDef.DirPath
- val outputFastqs: Boolean
- val platformModel: Option[String]
- val platformUnit: Option[String]
- val predictedInsertSize: Option[Integer]
- val qualityFormat: Option[FastqQualityFormat]
- val readStructures: Seq[ReadStructure]
- val runDate: Option[Iso8601Date]
- val sequencingCenter: Option[String]
- val sortOrder: SortOrder
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
- val threads: Int
-
def
toString(): String
- Definition Classes
- AnyRef → Any
- val umiTag: String
- val unmatched: String
-
def
validate(test: Boolean, message: ⇒ String): Unit
Generates a validation exception if the test value is false.
Generates a validation exception if the test value is false.
- Definition Classes
- FgBioTool
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
def
→[B](y: B): (DemuxFastqs, B)
- Implicit
- This member is added by an implicit conversion from DemuxFastqs to ArrowAssoc[DemuxFastqs] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc