Value Members

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.  def emptyIndex(inFiles: String*): Index

   Construct an empty index, using the supplied sequence files to prepare the minimizer ordering.

   Construct an empty index, using the supplied sequence files to prepare the minimizer ordering. This is useful when a frequency ordering is used and one wants to sample a large number of files in advance. Index.newCompatible or index(compatible: Index, inFiles: String*) can then be used to construct compatible indexes with actual k-mers using the resulting ordering.

   inFiles

   The input files to sample for frequency orderings

7.  final def eq(arg0: AnyRef): Boolean

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8.  def finalize(): Unit

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9.  final def getClass(): Class[_]

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10.  def getInputFragments(file: String, addRCReads: Boolean = false): Dataset[InputFragment]

    Single file version of the same method

11.  def getInputFragments(files: Seq[String], addRCReads: Boolean): Dataset[InputFragment]

    Load input fragments (with sequence title and location) according to the settings in this object.

    Load input fragments (with sequence title and location) according to the settings in this object.

    files

    input files

    addRCReads

    whether to add reverse complements

12.  def getInputSequences(file: String, addRCReads: Boolean = false): Dataset[NTSeq]

    Single file version of the same method

13.  def getInputSequences(files: Seq[String], addRCReads: Boolean): Dataset[NTSeq]

    Load reads/sequences from files according to the settings in this object.

    Load reads/sequences from files according to the settings in this object.

    files

    input files

    addRCReads

    whether to add reverse complements

14.  def getSplitter(inFiles: Option[Seq[String]], persistHash: Option[String] = None): MinSplitter[_ <: MinimizerPriorities]

    Construct a read splitter for the given input files based on the settings in this object.

    Construct a read splitter for the given input files based on the settings in this object.

    inFiles

    Input files (for frequency orderings, which require sampling)

    persistHash

    Location to persist the generated minimizer ordering (for frequency orderings), if any

    returns

    a MinSplitter configured with a minimizer ordering and corresponding MinTable

15.  def index(compatible: Index, inFiles: String*): Index

    Convenience method to construct a compatible counting k-mer index containing all k-mers from the input sequence files.

    Convenience method to construct a compatible counting k-mer index containing all k-mers from the input sequence files.

    compatible

    Compatible index to copy settings, such as an existing minimizer ordering, from

    inFiles

    input files

16.  def index(inFiles: String*): Index

    Convenience method to construct a counting k-mer index containing all k-mers from the input sequence files.

    Convenience method to construct a counting k-mer index containing all k-mers from the input sequence files. If a frequency minimizer ordering is used (which is the default), the input files will be sampled and a new minimizer ordering will be constructed.

    inFiles

    input files

17.  def inputReader(files: String*): Inputs

    Obtain an InputReader configured with settings from this object.

    Obtain an InputReader configured with settings from this object.

    files

    Files to read. Can be a single file or multiple files. Wildcards can be used. A name of the format @list.txt will be parsed as a list of files.

18.  final def isInstanceOf[T0]: Boolean

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19.  val k: Int
20.  def kmers(knownSplitter: Broadcast[AnyMinSplitter], inFiles: String*): Kmers

    Load k-mers from the given files.

21.  def kmers(inFiles: String*): Kmers

    Load k-mers from the given files.

22.  val m: Int
23.  val maxSequenceLength: Int
24.  val method: CountMethod
25.  val minimizers: MinimizerSource
26.  final def ne(arg0: AnyRef): Boolean

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27.  val normalize: Boolean
28.  final def notify(): Unit

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29.  final def notifyAll(): Unit

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30.  val ordering: MinimizerOrdering
31.  val partitions: Int
32.  val sample: Double
33.  def sequenceTitles(input: String*): Dataset[SeqTitle]

    Load sequence titles only from the given input files

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

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35.  final def wait(): Unit

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

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    @throws( ... )

37.  final def wait(arg0: Long): Unit

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