BaseCounter

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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

   

   Definition Classes

   BaseCounter → ToolCommand

6. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

7. def bamRecordBasesOverlap(samRecord: SAMRecord, start: Int, end: Int, counts: Counts, sense: Boolean): Int

   

8. def bamRecordBasesOverlap(samRecord: SAMRecord, start: Int, end: Int): Int

   

9. def clone(): AnyRef

   

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   protected[java.lang]

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

    

    Definition Classes

    ToolCommand

11. def contactText: String

    

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    ToolCommand

12. def contributingText: String

    

    Definition Classes

    ToolCommand

13. def createMetaExonCounts(genes: List[Gene]): List[(String, RegionCount)]

    

14. def descriptionText: String

    

    Definition Classes

    BaseCounter → ToolCommand

15. def documentationText: String

    

    Definition Classes

    ToolCommand

16. def emptyArgs: Args

    

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    BaseCounter → ToolCommand

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

    

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18. def equals(arg0: Any): Boolean

    

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

    

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    ToolCommand

20. def exampleText: String

    

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    BaseCounter → ToolCommand

21. def finalize(): Unit

    

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    protected[java.lang]

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

    

    Definition Classes

    ToolCommand

23. def generateMergedExonRegions(gene: Gene): BedRecordList

    

24. def generateReadme(outputFile: File): Unit

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    AnyRef → Any

26. def groupGenesOnOverlap(genes: Iterable[Gene]): Map[String, List[List[Gene]]]

    

27. def hashCode(): Int

    

    Definition Classes

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28. def installationText: String

    

    Definition Classes

    ToolCommand

29. final def isInstanceOf[T0]: Boolean

    

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    Any

30. def logger: Logger

    

    Definition Classes

    Logging

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

    

    Definition Classes

    BaseCounter → ToolCommand

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

    

    Definition Classes

    ToolCommand

33. def manualText: String

    

    Definition Classes

    BaseCounter → ToolCommand

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

    

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35. final def notify(): Unit

    

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36. final def notifyAll(): Unit

    

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    AnyRef

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

    

    Definition Classes

    ToolCommand

38. def samRecordStrand(samRecord: SAMRecord, strand: Boolean): Boolean

    

39. def samRecordStrand(samRecord: SAMRecord, gene: Gene): Boolean

    

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

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

    

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43. def toString(): String

    

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44. def toolName: String

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

46. def urlToolName: String

    

    Definition Classes

    ToolCommand

47. def usageText: String

    

    Definition Classes

    ToolCommand

48. final def wait(): Unit

    

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    @throws( ... )

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

    

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

    

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51. def writeExonCount(genes: List[GeneCount], outputDir: File, prefix: String): Unit

    

    This will write counts on each exon

52. def writeGeneCounts(genes: List[GeneCount], outputDir: File, prefix: String): Map[String, Map[String, Long]]

    

    This function will write all counts that are concatenated on gene level.

    This function will write all counts that are concatenated on gene level. Each line is 1 gene. Exonic: then it's seen as an exon on 1 of the transcripts Intronic: then it's not seen as an exon on 1 of the transcripts Exonic + Intronic = Total

53. def writeIntronCount(genes: List[GeneCount], outputDir: File, prefix: String): Unit

    

    This will write counts on each intron

54. def writeMergeExonCount(genes: List[GeneCount], outputDir: File, prefix: String): Unit

    

    This function will print all counts that exist on exonic regions, each base withing the gene is only represented once but all regions are separated

55. def writeMergeIntronCount(genes: List[GeneCount], outputDir: File, prefix: String): Unit

    

    This function will print all counts that do *not* exist on exonic regions, each base within the gene is only represented once but all regions are separated

56. def writeNonStrandedMetaExonsCount(metaCounts: List[(String, RegionCount)], outputDir: File, prefix: String): Unit

    

    This function will print all counts for meta exons

57. def writeStrandedMetaExonsCount(metaCounts: List[(String, RegionCount)], outputDir: File, prefix: String): Unit

    

    This function will print all counts for meta exons

58. def writeTranscriptCounts(genes: List[GeneCount], outputDir: File, prefix: String): Unit

    

    This function will write all counts that are concatenated on transcript level.

    This function will write all counts that are concatenated on transcript level. Each line is 1 transcript. Exonic: then it's seen as an exon on 1 of the transcripts Intronic: then it's not seen as an exon on 1 of the transcripts Exonic + Intronic = Total