SeqStat

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

   SeqStat → ToolCommand

6. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

7. var baseQualHistogram: ArrayBuffer[Long]

   

8. val baseStats: ArrayBuffer[BaseStat]

   

9. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

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

    

    Definition Classes

    ToolCommand

11. def contactText: String

    

    Definition Classes

    ToolCommand

12. def contributingText: String

    

    Definition Classes

    ToolCommand

13. def descriptionText: String

    

    Definition Classes

    SeqStat → ToolCommand

14. def detectPhredEncoding(quals: ArrayBuffer[Long]): Unit

    
    quals

    Computed quality histogram [flat]

15. def documentationText: String

    

    Definition Classes

    ToolCommand

16. def emptyArgs: Args

    

    Definition Classes

    SeqStat → ToolCommand

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

    

    Definition Classes

    AnyRef

18. def equals(arg0: Any): Boolean

    

    Definition Classes

    AnyRef → Any

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

    

    Definition Classes

    ToolCommand

20. def exampleText: String

    

    Definition Classes

    SeqStat → ToolCommand

21. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

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

    

    Definition Classes

    ToolCommand

23. def generateReadme(outputFile: File): Unit

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    AnyRef → Any

25. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

26. def installationText: String

    

    Definition Classes

    ToolCommand

27. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

28. def logger: Logger

    

    Definition Classes

    Logging

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

    

    Definition Classes

    SeqStat → ToolCommand

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

    

    Definition Classes

    ToolCommand

31. def manualText: String

    

    Definition Classes

    SeqStat → ToolCommand

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

    

    Definition Classes

    AnyRef

33. final def notify(): Unit

    

    Definition Classes

    AnyRef

34. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

35. var nucleotideHistoMap: Map[Char, Long]

    

36. var nucs: ArrayBuffer[Long]

    

37. var phredEncoding: FqEncoding.Value

    

38. def processRead(record: FastqRecord): Unit

    

    Compute the quality metric per read Results are stored in baseStats and readStats

    Compute the quality metric per read Results are stored in baseStats and readStats

    record

    FastqRecord

39. var quals: ArrayBuffer[Long]

    

40. var readLengthHistogram: Map[String, Long]

    

41. var readQualHistogram: ArrayBuffer[Long]

    

42. val readStats: ReadStat

    

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

    

    Definition Classes

    ToolCommand

44. def reportMap(fastqPath: File): Map[String, Any]

    

45. val reportValues: List[Int]

    

46. def seqStat(fqreader: FastqReader): Long

    

    seqStat, the compute entrypoint where all statistics collection starts

    seqStat, the compute entrypoint where all statistics collection starts

    fqreader

    FastqReader

    returns

    numReads - number of reads counted

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

49. def summarize(): Unit

    

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

    

    Definition Classes

    AnyRef

51. def toString(): String

    

    Definition Classes

    AnyRef → Any

52. def toolName: String

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

54. def urlToolName: String

    

    Definition Classes

    ToolCommand

55. def usageText: String

    

    Definition Classes

    ToolCommand

56. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )