Object

nl.biopet.tools.extractalignedfastq

ExtractAlignedFastq

Related Doc: package extractalignedfastq

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object ExtractAlignedFastq extends ToolCommand[Args]

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ToolCommand[Args], Logging, AnyRef, Any
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Type Members

  1. type FastqInput = (FastqRecord, Option[FastqRecord])

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    type alias for Fastq input (may or may not be paired)

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
    ExtractAlignedFastq → ToolCommand
  6. final def asInstanceOf[T0]: T0

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    Definition Classes
    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
    ExtractAlignedFastq → ToolCommand
  12. def documentationText: String

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    Definition Classes
    ToolCommand
  13. def emptyArgs: Args

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    Definition Classes
    ExtractAlignedFastq → 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
    ExtractAlignedFastq → ToolCommand
  18. def extractReads(memFunc: (FastqInput) ⇒ Boolean, inputFastq1: FastqReader, outputFastq1: BasicFastqWriter, inputFastq2: FastqReader, outputFastq2: BasicFastqWriter): Unit

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    Extracts reads from the given input Fastq pairs and writes to new output Fastq pair files

    Extracts reads from the given input Fastq pairs and writes to new output Fastq pair files

    memFunc

    Predicate for extracting reads. If evaluates to true, the read is extracted.

    inputFastq1

    Input FastqReader object for pair 1.

    outputFastq1

    Input FastqReader object for pair 2.

    inputFastq2

    Output BasicFastqWriter object for pair 1.

    outputFastq2

    Output BasicFastqWriter object for pair 2.

  19. def extractReads(memFunc: (FastqInput) ⇒ Boolean, inputFastq1: FastqReader, outputFastq1: BasicFastqWriter): Unit

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    Extracts reads from the given input Fastq file and writes to a new output Fastq file

    Extracts reads from the given input Fastq file and writes to a new output Fastq file

    memFunc

    Predicate for extracting reads. If evaluates to true, the read is extracted.

    inputFastq1

    Input FastqReader object.

    outputFastq1

    Output BasicFastqWriter object.

  20. def fastqId(rec: FastqRecord): String

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    Get the FastqRecord ID

  21. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  22. def generateDocumentation(outputDirectory: File, version: String, release: Boolean): Unit

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

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

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

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    Definition Classes
    AnyRef → Any
  26. def installationText: String

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

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    Definition Classes
    Any
  28. def logger: Logger

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

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    Definition Classes
    ExtractAlignedFastq → ToolCommand
  30. def mainPageContents: List[(String, String)]

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    Definition Classes
    ToolCommand
  31. def makeIntervalFromString(inStrings: Iterable[String]): Iterator[Interval]

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    Function to create iterator over Interval given input interval string

    Function to create iterator over Interval given input interval string

    Valid interval strings are either of these:

    • chr5:10000-11000
    • chr5:10,000-11,000
    • chr5:10.000-11.000
    • chr5:10000-11,000 In all cases above, the region span base #10,000 to base number #11,000 in chromosome 5 (first base is numbered 1)

    An interval string with a single base is also allowed:

    • chr5:10000
    • chr5:10,000
    • chr5:10.000
    inStrings

    iterable yielding input interval string

  32. def makeMembershipFunction(iv: Iterator[Interval], inAln: File, minMapQ: Int = 0, commonSuffixLength: Int = 0): (FastqInput) ⇒ Boolean

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    Function to create object that checks whether a given FASTQ record is mapped to the given interval or not

    Function to create object that checks whether a given FASTQ record is mapped to the given interval or not

    iv

    iterable yielding features to check

    inAln

    input SAM/BAM file

    minMapQ

    minimum mapping quality of read to include

    commonSuffixLength

    length of suffix common to all read pairs

  33. def manualText: String

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    Definition Classes
    ExtractAlignedFastq → ToolCommand
  34. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  35. final def notify(): Unit

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

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    Definition Classes
    AnyRef
  37. def readmeContents: List[(String, String)]

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

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

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    Definition Classes
    ToolCommand
  40. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  41. def toString(): String

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    Definition Classes
    AnyRef → Any
  42. def toolName: String

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

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    Definition Classes
    ToolCommand
  44. def urlToolName: String

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    Definition Classes
    ToolCommand
  45. def usageText: String

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

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

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

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    Definition Classes
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    @throws( ... )

Inherited from ToolCommand[Args]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

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