class FastqToBam extends FgBioTool with LazyLogging
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Instance Constructors
- new FastqToBam(input: Seq[commons.CommonsDef.PathToFastq], output: FgBioDef.PathToBam, readStructures: Seq[ReadStructure] = Seq(), sort: Boolean = false, umiTag: String = ConsensusTags.UmiBases, readGroupId: String = "A", sample: String, library: String, platform: String = "illumina", platformUnit: Option[String] = None, platformModel: Option[String] = None, sequencingCenter: Option[String] = None, predictedInsertSize: Option[Integer] = None, description: Option[String] = None, comment: List[String] = Nil, runDate: Option[Iso8601Date] = None)
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 FastqToBam to any2stringadd[FastqToBam] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
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def
->[B](y: B): (FastqToBam, B)
- Implicit
- This member is added by an implicit conversion from FastqToBam to ArrowAssoc[FastqToBam] performed by method ArrowAssoc in scala.Predef.
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- ArrowAssoc
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- @inline()
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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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- @throws( ... )
- val comment: List[String]
- val description: Option[String]
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def
ensuring(cond: (FastqToBam) ⇒ Boolean, msg: ⇒ Any): FastqToBam
- Implicit
- This member is added by an implicit conversion from FastqToBam to Ensuring[FastqToBam] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: (FastqToBam) ⇒ Boolean): FastqToBam
- Implicit
- This member is added by an implicit conversion from FastqToBam to Ensuring[FastqToBam] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): FastqToBam
- Implicit
- This member is added by an implicit conversion from FastqToBam to Ensuring[FastqToBam] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): FastqToBam
- Implicit
- This member is added by an implicit conversion from FastqToBam to Ensuring[FastqToBam] performed by method Ensuring in scala.Predef.
- Definition Classes
- 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
- FastqToBam → 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
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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
finalize(): Unit
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def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from FastqToBam to StringFormat[FastqToBam] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
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- @inline()
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final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- val input: 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
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final
def
isInstanceOf[T0]: Boolean
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- val library: String
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lazy val
logger: Logger
- Attributes
- protected
- Definition Classes
- LazyLogging
-
def
makeSamRecords(fqs: Seq[FastqRecord], structures: Seq[ReadStructure], header: SAMFileHeader, encoding: QualityEncoding): Seq[SamRecord]
Generates SamRecords for each of the template reads across the read structures.
Generates SamRecords for each of the template reads across the read structures.
- Attributes
- protected
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def
makeSamWriter(): SamWriter
Makes the SAMFileWriter we'll use to output the file.
Makes the SAMFileWriter we'll use to output the file.
- Attributes
- protected
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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.PathToBam
- val platform: String
- val platformModel: Option[String]
- val platformUnit: Option[String]
- val predictedInsertSize: Option[Integer]
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def
qualityEncoding: QualityEncoding
Determine the quality encoding of the incoming fastq files.
Determine the quality encoding of the incoming fastq files.
- Attributes
- protected
- val readGroupId: String
- val readStructures: Seq[ReadStructure]
- val runDate: Option[Iso8601Date]
- val sample: String
- val sequencingCenter: Option[String]
- val sort: Boolean
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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def
toString(): String
- Definition Classes
- AnyRef → Any
- val umiTag: String
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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.
- Definition Classes
- 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
- Definition Classes
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- @throws( ... )
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def
→[B](y: B): (FastqToBam, B)
- Implicit
- This member is added by an implicit conversion from FastqToBam to ArrowAssoc[FastqToBam] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc