AssemblyUtils

Value Members

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

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

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3. final def ##(): Int

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4. final def ==(arg0: AnyRef): Boolean

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

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6. final def asInstanceOf[T0]: T0

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7. def buildVariantsFromPath[T <: ReferenceVariant](path: Seq[Byte], referenceStart: Int, referenceContig: ContigSequence, alignPath: (Seq[Byte]) ⇒ ReadAlignment, buildVariant: (Int, Array[Byte], Array[Byte]) ⇒ T, allowReferenceVariant: Boolean = false): Seq[T]

   Call variants from a path discovered from the reads

   Call variants from a path discovered from the reads

   path

   Possible paths through the reads

   referenceStart

   Start locus on the reference contig or chromosome

   referenceContig

   Reference sequence overlapping the reference region

   alignPath

   Function that returns a ReadAlignment from the path

   buildVariant

   Function to build a called variant from the (Locus, ReferenceAllele, Alternate)

   allowReferenceVariant

   If true, output variants where the reference and alternate are the same

   returns

   Possible sequence of called variants

8. def clone(): AnyRef

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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. def discoverHaplotypes(currentWindow: SlidingWindow[MappedRead], kmerSize: Int, reference: ReferenceGenome, minOccurrence: Int, minMeanKmerQuality: Int, expectedPloidy: Int = 2, maxPathsToScore: Int = 16, debugPrint: Boolean = false): Seq[Seq[Byte]]

    currentWindow

    Window of reads that overlaps the current loci

    kmerSize

    Length kmers in the DeBruijn graph

    minOccurrence

    Minimum times a kmer must appear to be in the DeBruijn graph

    expectedPloidy

    Expected ploidy, or expected number of valid paths through the graph

    maxPathsToScore

    Number of paths to align to the reference to score them

    returns

    Collection of paths through the reads

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

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13. def equals(arg0: Any): Boolean

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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(msg: ⇒ Any, t: ⇒ Throwable): Unit

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20. def info(msg: ⇒ Any): Unit

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21. def isActiveRegion(reads: Seq[MappedRead], referenceContig: ContigSequence, minAreaVaf: Float): Boolean

    Heuristic to determine when a region has a complex collection of region alignments This is based on reads with multiple mismatches or insertion / deletion alignments

    Heuristic to determine when a region has a complex collection of region alignments This is based on reads with multiple mismatches or insertion / deletion alignments

    reads

    Set of reads in a reference region

    referenceContig

    Reference contig for the region

    minAreaVaf

    Minimum fraction of reads needed

    returns

    True if the 'active' region

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 logger: Logger

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29. def loggerName: String

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

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31. final def notify(): Unit

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32. final def notifyAll(): Unit

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

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34. def toString(): String

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

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36. def trace(msg: ⇒ Any): Unit

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37. final def wait(): Unit

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

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

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

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41. def warn(msg: ⇒ Any): Unit

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