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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

   

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5. def argsParser: ArgsParser

   

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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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10. def contributingText: String

    

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11. def descriptionText: String

    

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12. def documentationText: String

    

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13. def emptyArgs: Args

    

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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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17. def exampleText: String

    

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18. def extractStats(samRecordIterator: SAMRecordIterator, readgroupsMap: Map[String, GroupID], condition: (SAMRecord) ⇒ Boolean): BamstatsRoot

    

    This method iterates over all SAMrecords in the iterator and returns the groupstats The SAMRecordIterator is closed in this method.

    This method iterates over all SAMrecords in the iterator and returns the groupstats The SAMRecordIterator is closed in this method.

    samRecordIterator

    A samrecord iterator containing all the reads you are interested in. (I.e after a SAMReader.query)

    returns

    A GroupStats object with al the stats from the samrecords

19. def extractStatsAll(samReader: SamReader, readgroupsMap: Option[Map[String, GroupID]] = None): BamstatsRoot

    

    This methods reads the stats for all records in the SamReader.

    This methods reads the stats for all records in the SamReader. The samReader is not closed afterwards, so it can be reused.

    samReader

    A SamReader

    returns

    GroupStats for all records in the SamReader.

20. def extractStatsRegion(samReader: SamReader, region: BedRecord, readgroupsMap: Option[Map[String, GroupID]] = None, scatterMode: Boolean = false): BamstatsRoot

    

    Takes a samReader and retunrs the GroupStats for all reads in the described region

    Takes a samReader and retunrs the GroupStats for all reads in the described region

    samReader

    a SamReader

    region

    a BedRecord describing the region

    scatterMode

    if True, only reads that originate (i.e. have their start position) in the region are counted. This is useful when scattering over regions to make sure that reads are not counted twice. One time when the start position is in the region, and one time when the end position is in the region.

21. def extractStatsUnmappedReads(samReader: SamReader, readgroupsMap: Option[Map[String, GroupID]] = None): BamstatsRoot

    

    Takes a samReader and returns all the stats for all unmapped reads.

    Takes a samReader and returns all the stats for all unmapped reads.

    samReader

    a samReader

    returns

    GroupStats for all unmapped reads

22. def finalize(): Unit

    

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

    

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24. def generateReadme(outputFile: File): Unit

    

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

    

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26. def getReadGroupsMap(samReader: SamReader): Map[String, GroupID]

    

27. def hashCode(): Int

    

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28. def installationText: String

    

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29. final def isInstanceOf[T0]: Boolean

    

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30. def logger: Logger

    

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

    

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

    

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33. def manualText: String

    

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

    

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35. def newStatsMap(readgroups: Seq[String]): Map[String, GroupStats]

    

36. final def notify(): Unit

    

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37. final def notifyAll(): Unit

    

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

    

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

    

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

    

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

    

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42. def toString(): String

    

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43. def toolName: String

    

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

    

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45. def urlToolName: String

    

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46. def usageHeaders: List[String]

    

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47. def usageHtmlTable: String

    

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

    

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49. def usageText: String

    

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

    

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51. final def wait(): Unit

    

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

    

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

    

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54. def writeStatsToTsv(stats: GroupStats, outputDir: File): Unit

    

    Write GroupStats to tsv files

    Write GroupStats to tsv files

    stats

    a GroupStats object

    outputDir

    the directory where the tsv files are written.