org.anduril.runtime.table.io

FASTAGenome

class FASTAGenome extends Genome

A genome represented by a single FASTA file that is optionally indexed. If the index is present, it follows the Samtools format (five columns). When the FASTA file is genome.fa(sta), the index must be one of genome.fai, genome.fa.fai or genome.fasta.fai must be present. If the index is not present, the FASTA file is linearly scanned to obtain the indexing information. Note: currently, sequence queries are not supported for unindexed FASTA files.

Linear Supertypes
Genome, AnyRef, Any
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  1. FASTAGenome
  2. Genome
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Instance Constructors

  1. new FASTAGenome(fasta: File, chromosomeNormalizer: (String) ⇒ String = null)

Value Members

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

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

    Definition Classes
    Any
  3. final def ##(): Int

    Definition Classes
    AnyRef → Any
  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  5. final def ==(arg0: Any): Boolean

    Definition Classes
    Any
  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.

    Definition Classes
    Genome
  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any
  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.

    Definition Classes
    Genome
  9. val chromosomes: Seq[String]

    Return (normalized) chromosome names.

    Return (normalized) chromosome names.

    Definition Classes
    Genome
  10. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws()
  11. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  12. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any
  13. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws()
  14. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any
  15. 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.

    Definition Classes
    FASTAGenomeGenome
    Exceptions thrown
    UnsupportedOperationException

    If the genome implementation does not support sequence queries.

  16. def hashCode(): Int

    Definition Classes
    AnyRef → Any
  17. 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.

    Definition Classes
    Genome
  18. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  19. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  20. 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.

    Definition Classes
    Genome
  21. final def notify(): Unit

    Definition Classes
    AnyRef
  22. final def notifyAll(): Unit

    Definition Classes
    AnyRef
  23. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef
  24. def toString(): String

    Definition Classes
    AnyRef → Any
  25. def totalLength(): Long

    Return the sum of chromosome lengths.

    Return the sum of chromosome lengths.

    Definition Classes
    Genome
  26. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws()
  27. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws()
  28. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws()

Inherited from Genome

Inherited from AnyRef

Inherited from Any

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