Object

nl.biopet.tools.fastqsync

FastqSync

Related Doc: package fastqsync

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object FastqSync extends ToolCommand[Args]

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ToolCommand[Args], Logging, AnyRef, Any
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  1. FastqSync
  2. ToolCommand
  3. Logging
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Value Members

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

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

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    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  4. def aboutText: String

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    Definition Classes
    ToolCommand
  5. def argsParser: ArgsParser

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    Definition Classes
    FastqSync → ToolCommand
  6. final def asInstanceOf[T0]: T0

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    Any
  7. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  8. def cmdArrayToArgs(args: Array[String]): Args

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    Definition Classes
    ToolCommand
  9. def contactText: String

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    Definition Classes
    ToolCommand
  10. def contributingText: String

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    Definition Classes
    ToolCommand
  11. def descriptionText: String

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    Definition Classes
    FastqSync → ToolCommand
  12. def documentationText: String

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    Definition Classes
    ToolCommand
  13. def emptyArgs: Args

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    Definition Classes
    FastqSync → ToolCommand
  14. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  15. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  16. def example(args: String*): String

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    Definition Classes
    ToolCommand
  17. def exampleText: String

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    Definition Classes
    FastqSync → ToolCommand
  18. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  19. def findR1R2Suffixes(fastqR1: File, fastqR2: File): (String, String)

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    This method will look up the unique suffix for R1 and R2

    This method will look up the unique suffix for R1 and R2

    fastqR1

    input R1 file

    fastqR2

    Input R2 file

    returns

    suffix for (R1, R2)

  20. def generateDocumentation(outputDirectory: File, version: String, release: Boolean): Unit

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    Definition Classes
    ToolCommand
  21. def generateReadme(outputFile: File): Unit

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    Definition Classes
    ToolCommand
  22. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  23. def hashCode(): Int

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    AnyRef → Any
  24. def installationText: String

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    Definition Classes
    ToolCommand
  25. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  26. def logger: Logger

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    Definition Classes
    Logging
  27. def main(args: Array[String]): Unit

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    Definition Classes
    FastqSync → ToolCommand
  28. def mainPageContents: List[(String, String)]

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    Definition Classes
    ToolCommand
  29. def manualText: String

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    Definition Classes
    FastqSync → ToolCommand
  30. final def ne(arg0: AnyRef): Boolean

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    AnyRef
  31. final def notify(): Unit

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    Definition Classes
    AnyRef
  32. final def notifyAll(): Unit

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    AnyRef
  33. def readmeContents: List[(String, String)]

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    Definition Classes
    ToolCommand
  34. def sparkExample(args: String*): String

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    Definition Classes
    ToolCommand
  35. def sparkUnsafeExample(args: String*): String

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    Definition Classes
    ToolCommand
  36. def syncFastq(pre: FastqReader, seqA: FastqReader, seqB: FastqReader, seqOutA: AsyncFastqWriter, seqOutB: AsyncFastqWriter): (Long, Long, Long)

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    Filters out FastqRecord that are not present in the input iterators, using a reference sequence object

    Filters out FastqRecord that are not present in the input iterators, using a reference sequence object

    pre

    FastqReader over reference FASTQ file

    seqA

    FastqReader over read 1

    seqB

    FastqReader over read 2

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

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    Definition Classes
    AnyRef
  38. def toString(): String

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    Definition Classes
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  39. def toolName: String

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    Definition Classes
    ToolCommand
  40. def unsafeExample(args: String*): String

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    Definition Classes
    ToolCommand
  41. def urlToolName: String

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    Definition Classes
    ToolCommand
  42. def usageHeaders: List[String]

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    Attributes
    protected
    Definition Classes
    ToolCommand
  43. def usageHtmlTable: String

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    Definition Classes
    ToolCommand
  44. def usageRows(parser: OptionParser[Args]): List[List[String]]

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    Attributes
    protected
    Definition Classes
    ToolCommand
  45. def usageText: String

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    Definition Classes
    ToolCommand
  46. def validateArgs(args: String*): Unit

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    Definition Classes
    ToolCommand
  47. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  48. final def wait(arg0: Long, arg1: Int): Unit

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    Annotations
    @throws( ... )
  49. final def wait(arg0: Long): Unit

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    Definition Classes
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    Annotations
    @throws( ... )

Inherited from ToolCommand[Args]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

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