FlagStats

Value Members

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

   

   Definition Classes

   AnyRef → Any

2. final def ##(): Int

   

   Definition Classes

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3. def +=(other: FlagStats): Unit

   

   Add another flagstats instance

   Add another flagstats instance

   other

   another FlagStats instance

4. def ==(other: FlagStats): Boolean

   

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

   

   Definition Classes

   AnyRef → Any

6. def addFlagStatsData(flagStatsData: FlagStatsData): Unit

   

   Method to add FlagStatsData which can be read from JSON

   Method to add FlagStatsData which can be read from JSON

   flagStatsData

   the FlagStatsData

7. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

8. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

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   Annotations

   @throws( ... )

9. def crossCountsSortedMethods: List[(FlagMethods.Value, List[(FlagMethods.Value, Long)])]

   

   * Returns a crosscount table with methods

   * Returns a crosscount table with methods

   returns

   a sorted list of methods with crosscounts.

10. def crossCountsSortedNames: List[(String, List[(String, Long)])]

    

    Returns a crosscount table with names

    Returns a crosscount table with names

    returns

    a sorted list of names with crosscounts.

11. def crossCountsToMap: Map[String, Map[String, Long]]

    

    Converts crosscounts to a map

    Converts crosscounts to a map

    returns

    a map with method names as a key and flagstats maps as values

12. def crossReport(fraction: Boolean = false): String

    

    This returns a tsv table.

    This returns a tsv table. All the flag ids are in the first row and the first column. The table body contains counts

    fraction

    use percentages instead of counts

    returns

    a tsv table

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

    

    Definition Classes

    AnyRef

14. def equals(arg0: Any): Boolean

    

    Definition Classes

    AnyRef → Any

15. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

16. def flagStatsToMap: Map[String, Long]

    

    Convert flagstats to a map

    Convert flagstats to a map

    returns

    a map with method names as a key and counts as value.

17. def flagstatsSortedMethods: List[(FlagMethods.Value, Long)]

    

    Method to return flagstats with methods.

    Method to return flagstats with methods.

    returns

    a sorted list of flagstats with methods

18. def flagstatsSortedNames: List[(String, Long)]

    

    Method to return flagstats with names.

    Method to return flagstats with names.

    returns

    a sorted list of flagstats with names

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

    

    Definition Classes

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20. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

21. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

22. def loadRecord(record: SAMRecord): Unit

    

    Loads one SAMrecord and tests it for the flags.

    Loads one SAMrecord and tests it for the flags. Then updates the internal flagstats and crosscounts counters

    record

    a SAMrecord

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

    

    Definition Classes

    AnyRef

24. final def notify(): Unit

    

    Definition Classes

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25. final def notifyAll(): Unit

    

    Definition Classes

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26. def report(): String

    

    A report that includes a table of the flagstats including percentages.

    A report that includes a table of the flagstats including percentages. Also includes crosscounts with raw numbers and percentages

    returns

    a string containing the report

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

    

    Definition Classes

    AnyRef

28. def toFlagStatsData: FlagStatsData

    

    Returns a FlagStatsData object that can be serialized into data.

    Returns a FlagStatsData object that can be serialized into data.

    returns

    a FlagStatsData object

29. def toString(): String

    

    Definition Classes

    AnyRef → Any

30. def toSummaryJson(includeCrossCounts: Boolean = true): String

    
    returns

    A json string with the summary

31. def toSummaryMap(includeCrossCounts: Boolean = true): Map[String, Any]

    

    Create a summary map of the gathered counts

    Create a summary map of the gathered counts

    includeCrossCounts

    Whether Crosscounts should be included in the summary

    returns

    a summary map

32. def totalReads: Long

    

    Gets the total number of reads by reading it from the flagstats array

    Gets the total number of reads by reading it from the flagstats array

    returns

    the total number of reads.

33. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

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    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

36. def writeAsTsv(file: File): Unit

    

    Write a TSV file with names in the first column and counts in the second.

    Write a TSV file with names in the first column and counts in the second.

    file

    the output file

37. def writeReportToFile(outputFile: File): Unit

    

    Write the report to file

    Write the report to file

    outputFile

    the file to which the report will be written.

38. def writeSummaryToFile(outputFile: File, includeCrossCounts: Boolean = true): Unit

    

    Write the summary map to a tsv file

    Write the summary map to a tsv file

    outputFile

    the file

    includeCrossCounts

    whether crosscunts should be included.