WipeReads

Value Members

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

   

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2. final def ##(): Int

   

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

   

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4. def aboutText: String

   

   Definition Classes

   ToolCommand

5. def argsParser: ArgsParser

   

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   WipeReads → ToolCommand

6. final def asInstanceOf[T0]: T0

   

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7. def clone(): AnyRef

   

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   protected[java.lang]

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8. def cmdArrayToArgs(args: Array[String]): Args

   

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9. def contactText: String

   

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   ToolCommand

10. def contributingText: String

    

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    ToolCommand

11. def descriptionText: String

    

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    WipeReads → ToolCommand

12. def documentationText: String

    

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    ToolCommand

13. def emptyArgs: Args

    

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    WipeReads → ToolCommand

14. final def eq(arg0: AnyRef): Boolean

    

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15. def equals(arg0: Any): Boolean

    

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16. def example(args: String*): String

    

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    ToolCommand

17. def exampleText: String

    

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    WipeReads → ToolCommand

18. def finalize(): Unit

    

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

    

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    ToolCommand

20. def generateReadme(outputFile: File): Unit

    

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    ToolCommand

21. final def getClass(): Class[_]

    

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22. def hashCode(): Int

    

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23. def installationText: String

    

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    ToolCommand

24. final def isInstanceOf[T0]: Boolean

    

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25. def logger: Logger

    

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    Logging

26. def main(args: Array[String]): Unit

    

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    WipeReads → ToolCommand

27. def mainPageContents: List[(String, String)]

    

    Definition Classes

    ToolCommand

28. def makeFilterNotFunction(ivl: List[Interval], inBam: File, filterOutMulti: Boolean = true, minMapQ: Int = 0, readGroupIds: Set[String] = Set(), bloomSize: Long, bloomFp: Double): (SAMRecord) ⇒ Boolean

    

    Function to create function to check SAMRecord for exclusion in filtered BAM file.

    Function to create function to check SAMRecord for exclusion in filtered BAM file.

    The returned function evaluates all filtered-in SAMRecord to false.

    ivl

    iterator yielding Feature objects

    inBam

    input BAM file

    filterOutMulti

    whether to filter out reads with same name outside target region (default: true)

    minMapQ

    minimum MapQ of reads in target region to filter out (default: 0)

    readGroupIds

    read group IDs of reads in target region to filter out (default: all IDs)

    bloomSize

    expected size of elements to contain in the Bloom filter

    bloomFp

    expected Bloom filter false positive rate

    returns

    function that checks whether a SAMRecord or String is to be excluded

29. def makeIntervalFromFile(inFile: File, gtfFeatureType: String = "exon"): List[Interval]

    

    Creates a list of intervals given an input File

    Creates a list of intervals given an input File

    inFile

    input interval file

30. def manualText: String

    

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    WipeReads → ToolCommand

31. final def ne(arg0: AnyRef): Boolean

    

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32. final def notify(): Unit

    

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33. final def notifyAll(): Unit

    

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34. def readmeContents: List[(String, String)]

    

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    ToolCommand

35. def sparkExample(args: String*): String

    

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    ToolCommand

36. def sparkUnsafeExample(args: String*): String

    

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    ToolCommand

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

    

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38. def toString(): String

    

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39. def toolName: String

    

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    ToolCommand

40. def unsafeExample(args: String*): String

    

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    ToolCommand

41. def urlToolName: String

    

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    ToolCommand

42. def usageHeaders: List[String]

    

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    protected

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43. def usageHtmlTable: String

    

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

    

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45. def usageText: String

    

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    ToolCommand

46. def validateArgs(args: String*): Unit

    

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    ToolCommand

47. final def wait(): Unit

    

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48. final def wait(arg0: Long, arg1: Int): Unit

    

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

    

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50. def writeFilteredBam(filterFunc: (SAMRecord) ⇒ Boolean, inBam: SamReader, outBam: SAMFileWriter, filteredOutBam: Option[SAMFileWriter] = None): Unit

    

    Function to filter input BAM and write its output to the filesystem

    Function to filter input BAM and write its output to the filesystem

    filterFunc

    filter function that evaluates true for excluded SAMRecord

    inBam

    input BAM file

    outBam

    output BAM file

    filteredOutBam

    whether to write excluded SAMRecords to their own BAM file