Class/Object

org.bdgenomics.adam.rdd.fragment

Tab5InFormatter

Related Docs: object Tab5InFormatter | package fragment

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class Tab5InFormatter extends InFormatter[Fragment, FragmentRDD, Tab5InFormatter] with Logging

Linear Supertypes
Logging, InFormatter[Fragment, FragmentRDD, Tab5InFormatter], Serializable, Serializable, AnyRef, Any
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Inherited
  1. Tab5InFormatter
  2. Logging
  3. InFormatter
  4. Serializable
  5. Serializable
  6. AnyRef
  7. Any
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Value Members

  1. final def !=(arg0: Any): Boolean

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    AnyRef → Any
  2. final def ##(): Int

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  3. final def ==(arg0: Any): Boolean

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  4. final def asInstanceOf[T0]: T0

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  5. def clone(): AnyRef

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    Attributes
    protected[java.lang]
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    AnyRef
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    @throws( ... )
  6. val companion: Tab5InFormatter.type

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    Attributes
    protected
    Definition Classes
    Tab5InFormatterInFormatter
  7. final def eq(arg0: AnyRef): Boolean

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    AnyRef
  8. def equals(arg0: Any): Boolean

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  9. def finalize(): Unit

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    protected[java.lang]
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    @throws( classOf[java.lang.Throwable] )
  10. final def getClass(): Class[_]

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  11. def hashCode(): Int

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  12. final def isInstanceOf[T0]: Boolean

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  13. def isTraceEnabled(): Boolean

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    protected
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    Logging
  14. def log: Logger

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    Logging
  15. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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    Logging
  16. def logDebug(msg: ⇒ String): Unit

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    Logging
  17. def logError(msg: ⇒ String, throwable: Throwable): Unit

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    Logging
  18. def logError(msg: ⇒ String): Unit

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    Logging
  19. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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    Logging
  20. def logInfo(msg: ⇒ String): Unit

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    Logging
  21. def logName: String

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    Logging
  22. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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    Logging
  23. def logTrace(msg: ⇒ String): Unit

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    Logging
  24. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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    Logging
  25. def logWarning(msg: ⇒ String): Unit

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    Logging
  26. final def ne(arg0: AnyRef): Boolean

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  27. final def notify(): Unit

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    AnyRef
  28. final def notifyAll(): Unit

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  29. final def synchronized[T0](arg0: ⇒ T0): T0

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  30. def toString(): String

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  31. final def wait(): Unit

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    @throws( ... )
  32. final def wait(arg0: Long, arg1: Int): Unit

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  33. final def wait(arg0: Long): Unit

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  34. def write(os: OutputStream, iter: Iterator[Fragment]): Unit

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    Writes alignment records to an output stream in Bowtie tab5 format.

    Writes alignment records to an output stream in Bowtie tab5 format.

    In Bowtie tab5 format, each alignment record or pair is on a single line. An unpaired alignment record line is [name]\t[seq]\t[qual]\n. A paired-end read line is [name]\t[seq1]\t[qual1]\t[seq2]\t[qual2]\n.

    The read name for a paired-end read line is the name of the first read with the suffix trimmed.

    os

    An OutputStream connected to a process we are piping to.

    iter

    An iterator of records to write.

    Definition Classes
    Tab5InFormatterInFormatter

Inherited from Logging

Inherited from InFormatter[Fragment, FragmentRDD, Tab5InFormatter]

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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