org.anduril.runtime.table.io

Genome

class Genome extends AnyRef

Base class for genome representations. A genome consists of a set of chromosome names, lengths, and nucleotide sequences. The genome may represent a reference genome, or the assembly of an individual genome (e.g., as a set of contigs).

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Instance Constructors

  1. new Genome(chromosomeNormalizer: (String) ⇒ String = null)

    chromosomeNormalizer

    A function that is used to normalize chromosome names, or null if no normalization should be done. The Genome companion object contains ready-made normalization functions.

Value Members

  1. final def !=(arg0: AnyRef): 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. def addChromosome(name: String, length: Long): Unit

    Register a new chromosome to the genome

    Register a new chromosome to the genome

    name

    Chromosome name (unique identifier).

    length

    Number of nucleotides in the chromosome.

  7. final def asInstanceOf[T0]: T0

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  8. def chromosomeLength(chromosome: String): Long

    Return the length of given chromosome, or -1 if the chromosome does not exist.

    Return the length of given chromosome, or -1 if the chromosome does not exist.

    chromosome

    Chromosome name; can be normalized or not.

  9. val chromosomeNormalizer: (String) ⇒ String

    A function that is used to normalize chromosome names, or null if no normalization should be done.

    A function that is used to normalize chromosome names, or null if no normalization should be done. The Genome companion object contains ready-made normalization functions.

  10. val chromosomes: Seq[String]

    Return (normalized) chromosome names.

  11. def clone(): AnyRef

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

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  14. def finalize(): Unit

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

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  16. def getSequence(chromosome: String, start: Long, length: Long): String

    Return the nucleotide sequence of the given location.

    Return the nucleotide sequence of the given location. The default implementation throws UnsupportedOperationException.

    chromosome

    Chromosome name.

    start

    Start position for query; the first base has index 1.

    length

    Length of the query. The result contains at most this many symbols. Length can legally extend past the end of the sequence, in which case it is truncated.

    Exceptions thrown
    UnsupportedOperationException

    If the genome implementation does not support sequence queries.

  17. def hashCode(): Int

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  18. def incChromosomeLength(name: String, lengthIncrease: Long): Unit

    Increase the length of a chromosome in the genome.

    Increase the length of a chromosome in the genome. If the chromosome does not exist, it is added.

    name

    Chromosome name (unique identifier).

    lengthIncrease

    Length increment as a number of nucleotides.

  19. final def isInstanceOf[T0]: Boolean

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

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  21. def normalizedChromosome(name: String): String

    Normalize the given chromosome name.

    Normalize the given chromosome name. If the chromosomeNormalizer value is null, return the name unchanged.

  22. final def notify(): Unit

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  23. final def notifyAll(): Unit

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

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  25. def toString(): String

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  26. def totalLength(): Long

    Return the sum of chromosome lengths.

  27. final def wait(): Unit

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

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

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