class CollectDuplexSeqMetrics extends FgBioTool with LazyLogging
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Instance Constructors
- new CollectDuplexSeqMetrics(input: FgBioDef.PathToBam, output: FgBioDef.PathPrefix, intervals: Option[FgBioDef.PathToIntervals] = None, description: Option[String] = None, duplexUmiCounts: Boolean = false, minAbReads: Int = 1, minBaReads: Int = 1, generatePlots: Boolean = true)
Value Members
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from CollectDuplexSeqMetrics to any2stringadd[CollectDuplexSeqMetrics] performed by method any2stringadd in scala.Predef.
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- any2stringadd
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def
->[B](y: B): (CollectDuplexSeqMetrics, B)
- Implicit
- This member is added by an implicit conversion from CollectDuplexSeqMetrics to ArrowAssoc[CollectDuplexSeqMetrics] performed by method ArrowAssoc in scala.Predef.
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final
def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
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def
clone(): AnyRef
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def
collect(iterator: Iterator[SamRecord]): Unit
Consumes from the iterator and collects information internally from which to generate metrics.
- val description: Option[String]
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def
duplexFamilySizeMetrics: Seq[DuplexFamilySizeMetric]
Generates the duplex family size metrics from the current observations.
- val duplexUmiCounts: Boolean
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def
duplexUmiMetrics(umiMetrics: Seq[UmiMetric]): Seq[DuplexUmiMetric]
Generates the duplex UMI metrics from the current observations.
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def
ensuring(cond: (CollectDuplexSeqMetrics) ⇒ Boolean, msg: ⇒ Any): CollectDuplexSeqMetrics
- Implicit
- This member is added by an implicit conversion from CollectDuplexSeqMetrics to Ensuring[CollectDuplexSeqMetrics] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: (CollectDuplexSeqMetrics) ⇒ Boolean): CollectDuplexSeqMetrics
- Implicit
- This member is added by an implicit conversion from CollectDuplexSeqMetrics to Ensuring[CollectDuplexSeqMetrics] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: Boolean, msg: ⇒ Any): CollectDuplexSeqMetrics
- Implicit
- This member is added by an implicit conversion from CollectDuplexSeqMetrics to Ensuring[CollectDuplexSeqMetrics] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: Boolean): CollectDuplexSeqMetrics
- Implicit
- This member is added by an implicit conversion from CollectDuplexSeqMetrics to Ensuring[CollectDuplexSeqMetrics] performed by method Ensuring in scala.Predef.
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- Ensuring
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final
def
eq(arg0: AnyRef): Boolean
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def
equals(arg0: Any): Boolean
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def
execute(): Unit
- Definition Classes
- CollectDuplexSeqMetrics → FgBioTool
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def
fail(exit: Int, message: String): Nothing
Fail with a specific error code and message.
Fail with a specific error code and message.
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- FgBioTool
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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
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def
fail(exit: Int): Nothing
Fail with just an exit code.
Fail with just an exit code.
- Definition Classes
- FgBioTool
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def
familySizeMetrics: Seq[FamilySizeMetric]
Generates the family size metrics from the current observations.
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def
finalize(): Unit
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def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from CollectDuplexSeqMetrics to StringFormat[CollectDuplexSeqMetrics] performed by method StringFormat in scala.Predef.
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- StringFormat
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- @inline()
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final
def
getClass(): Class[_]
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def
hashCode(): Int
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- val input: FgBioDef.PathToBam
- val intervals: Option[FgBioDef.PathToIntervals]
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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
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final
def
isInstanceOf[T0]: Boolean
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lazy val
logger: Logger
- Attributes
- protected
- Definition Classes
- LazyLogging
- val minAbReads: Int
- val minBaReads: Int
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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
- Definition Classes
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- val output: FgBioDef.PathPrefix
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def
pDuplexIdeal(reads: Int): Double
For a given family size/number of reads computes the probability that we would observed at least minAb & minBa reads under a binomial sampling model with p=0.5.
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
- Definition Classes
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def
umiMetrics: Seq[UmiMetric]
Generates the UMI metrics from the current observations.
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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.
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- FgBioTool
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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
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def
yieldMetrics: Seq[DuplexYieldMetric]
Generates the duplex yield metrics from the current observations.
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def
→[B](y: B): (CollectDuplexSeqMetrics, B)
- Implicit
- This member is added by an implicit conversion from CollectDuplexSeqMetrics to ArrowAssoc[CollectDuplexSeqMetrics] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc