BamStats

Value Members

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

   

   Definition Classes

   AnyRef → Any

2. final def ##(): Int

   

   Definition Classes

   AnyRef → Any

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

   

   Definition Classes

   AnyRef → Any

4. def aboutText: String

   

   Definition Classes

   ToolCommand

5. def argsParser: ArgsParser

   

   Definition Classes

   BamStats → ToolCommand

6. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

7. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

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

   

   Definition Classes

   ToolCommand

9. def contactText: String

   

   Definition Classes

   ToolCommand

10. def contributingText: String

    

    Definition Classes

    ToolCommand

11. def descriptionText: String

    

    Definition Classes

    BamStats → ToolCommand

12. def documentationText: String

    

    Definition Classes

    ToolCommand

13. def emptyArgs: Args

    

    Definition Classes

    BamStats → ToolCommand

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

    

    Definition Classes

    AnyRef

15. def equals(arg0: Any): Boolean

    

    Definition Classes

    AnyRef → Any

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

    

    Definition Classes

    ToolCommand

17. def exampleText: String

    

    Definition Classes

    BamStats → ToolCommand

18. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

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

    

    Definition Classes

    ToolCommand

20. def generateReadme(outputFile: File): Unit

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    AnyRef → Any

22. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

23. def init(outputDir: File, bamFile: File, referenceDict: SAMSequenceDictionary, binSize: Int, threadBinSize: Int, tsvOutput: Boolean): Unit

    

    This is the main running function of BamStats.

    This is the main running function of BamStats. This will start the threads and collect and write the results.

    outputDir

    All output files will be placed here

    bamFile

    Input bam file

    referenceDict

    Dict for scattering

    binSize

    stats binsize

    threadBinSize

    Thread binsize

24. def installationText: String

    

    Definition Classes

    ToolCommand

25. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

26. def logger: Logger

    

    Definition Classes

    Logging

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

    

    Definition Classes

    BamStats → ToolCommand

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

    

    Definition Classes

    ToolCommand

29. def manualText: String

    

    Definition Classes

    BamStats → ToolCommand

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

    

    Definition Classes

    AnyRef

31. final def notify(): Unit

    

    Definition Classes

    AnyRef

32. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

33. def processRegion(bedRecord: BedRecord, samReader: SamReader): Stats

    

34. def processThread(scatters: List[BedRecord], bamFile: File): Future[Map[BedRecord, Stats]]

    

    This method will process 1 thread bin

    This method will process 1 thread bin

    scatters

    bins to check, there should be no gaps withing the scatters

    bamFile

    Input bamfile

    returns

    Output stats

35. def processUnmappedReads(bamFile: File): Future[Stats]

    

    This method will only count the unmapped fragments

    This method will only count the unmapped fragments

    bamFile

    Input bamfile

    returns

    Output stats

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    AnyRef

40. def toString(): String

    

    Definition Classes

    AnyRef → Any

41. def toolName: String

    

    Definition Classes

    ToolCommand

42. def tsvToMap(tsvFile: File): Map[String, Array[Long]]

    

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

    

    Definition Classes

    ToolCommand

44. def urlToolName: String

    

    Definition Classes

    ToolCommand

45. def usageText: String

    

    Definition Classes

    ToolCommand

46. def validateReferenceInBam(bamFile: File, referenceFasta: Option[File]): SAMSequenceDictionary

    

    This will retrieve the SAMSequenceDictionary from the bam file.

    This will retrieve the SAMSequenceDictionary from the bam file. When referenceFasta is given he will validate this against the bam file.

47. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

50. def waitOnFutures(futures: List[Future[Map[BedRecord, Stats]]], msg: Option[String] = None): (Stats, Map[String, Stats])

    

    This method will wait when all futures are complete and collect a single Stats instance

    This method will wait when all futures are complete and collect a single Stats instance

    futures

    List of futures to monitor

    msg

    Optional message for logging

    returns

    Output stats