LoadBamContext

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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. final def asInstanceOf[T0]: T0

   

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5. def clone(): AnyRef

   

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6. implicit def conf: Configuration

   

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   CanLoadBam

7. val ctx: Context

   

8. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

   

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9. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

   

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10. def debug(msg: ⇒ Any): Unit

    

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

    

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12. def equals(arg0: Any): Boolean

    

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13. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    

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14. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

    

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15. def error(msg: ⇒ Any): Unit

    

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16. def finalize(): Unit

    

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

    

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18. def hashCode(): Int

    

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19. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    

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20. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

    

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21. def info(msg: ⇒ Any): Unit

    

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22. def isDebugEnabled: Boolean

    

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23. def isErrorEnabled: Boolean

    

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24. def isInfoEnabled: Boolean

    

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25. final def isInstanceOf[T0]: Boolean

    

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26. def isTraceEnabled: Boolean

    

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27. def isWarnEnabled: Boolean

    

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28. def loadBam(path: Path, splitSize: MaxSplitSize = MaxSplitSize(), bgzfBlocksToCheck: BGZFBlocksToCheck = ..., readsToCheck: ReadsToCheck = `package`.this.ReadsToCheck.default, maxReadSize: MaxReadSize = `package`.this.MaxReadSize.default): RDD[SAMRecord]

    

    Definition Classes

    CanLoadBam

29. def loadBamIntervals(path: Path, intervals: LociSet)(implicit splitSize: MaxSplitSize, r: EstimatedCompressionRatio): RDD[SAMRecord]

    

    Definition Classes

    Intervals

30. def loadBamIntervals(path: Path, intervals: String*)(implicit splitSize: MaxSplitSize, ratio: EstimatedCompressionRatio): RDD[SAMRecord]

    

    Definition Classes

    Intervals

31. def loadBamIntervals(path: Path, splitSize: MaxSplitSize = MaxSplitSize(), estimatedCompressionRatio: EstimatedCompressionRatio = ...)(intervals: String*): RDD[SAMRecord]

    

    Load SAMRecords that overlap specific genomic intervals from an indexed BAM file.

    Load SAMRecords that overlap specific genomic intervals from an indexed BAM file.

    path

    Indexed BAM file path

    splitSize

    divide the loaded file-portions into partitions of approximately this (uncompressed) size

    estimatedCompressionRatio

    used for (approximately) sizing returned partitions: compressed sizes of BAI "chunks" are scaled by this value so that returned partitions are – theoretically/approximately – splitSize (uncompressed)

    intervals

    Genomic intervals to intersect with

    returns

    RDD of SAMRecords that overlap the provided LociSet

    Definition Classes

    Intervals

32. def loadReads(path: Path, bgzfBlocksToCheck: BGZFBlocksToCheck = ..., readsToCheck: ReadsToCheck = `package`.this.ReadsToCheck.default, maxReadSize: MaxReadSize = `package`.this.MaxReadSize.default, splitSize: MaxSplitSize = MaxSplitSize()): RDD[SAMRecord]

    

    Load reads from a .sam, .bam, or .cram file

    Load reads from a .sam, .bam, or .cram file

    path

    Path to a .sam or .bam file

    bgzfBlocksToCheck

    when searching for bgzf-block-boundaries, check this many blocks ahead before declaring a position to be a block-boundary

    readsToCheck

    number of successive reads to verify before emitting a record-/split-boundary

    maxReadSize

    when searching for BAM-record-boundaries, try up to this many consecutive positions before giving up / throwing; reads taking up more than this many bytes on disk can result in "false-negative" read-boundary calls

    splitSize

    maximum (compressed) size of generated partitions

    Definition Classes

    CanLoadBam

33. def loadReadsAndPositions(path: Path, splitSize: MaxSplitSize = MaxSplitSize(), bgzfBlocksToCheck: BGZFBlocksToCheck = ..., readsToCheck: ReadsToCheck = `package`.this.ReadsToCheck.default, maxReadSize: MaxReadSize = `package`.this.MaxReadSize.default): RDD[(Pos, SAMRecord)]

    

    Definition Classes

    CanLoadBam

34. def loadSam(path: Path, splitSize: MaxSplitSize = MaxSplitSize()): RDD[SAMRecord]

    

    Load an RDD of SAMRecords from a SAM-file Path.

    Load an RDD of SAMRecords from a SAM-file Path.

    Definition Classes

    CanLoadBam

35. def loadSplitsAndReads(path: Path, splitSize: MaxSplitSize = MaxSplitSize(), bgzfBlocksToCheck: BGZFBlocksToCheck = ..., readsToCheck: ReadsToCheck = `package`.this.ReadsToCheck.default, maxReadSize: MaxReadSize = `package`.this.MaxReadSize.default): BAMRecordRDD

    

    Definition Classes

    CanLoadBam

36. def logger: Logger

    

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37. def loggerName: String

    

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

    

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39. final def notify(): Unit

    

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40. final def notifyAll(): Unit

    

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41. implicit def sc: SparkContext

    

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    LoadBamContext → CanLoadBam

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

    

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43. def toString(): String

    

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44. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    

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45. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

    

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46. def trace(msg: ⇒ Any): Unit

    

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47. final def wait(): Unit

    

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

    

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

    

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50. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    

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51. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

    

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52. def warn(msg: ⇒ Any): Unit

    

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