Package org.snpeff.interval

Class Genome

java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Genome
All Implemented Interfaces:
Serializable, Cloneable, Comparable<Interval>, Iterable<Chromosome>, TxtSerializable
public class Genome extends Marker implements Iterable<Chromosome>
This is just used for the Interval class. It is NOT a representation of an entire genome.
Author:
pcingola
See Also:

  • Constructor Details

    • Genome

      public Genome()

    • Genome

      public Genome(String version)

    • Genome

      public Genome(String version, Config config)

  • Method Details

    • createFromFaidx

      public static Genome createFromFaidx(String genomeName, String faidxFile)
      Create a genome from a faidx file. See "samtools faidx" command (reference http://samtools.sourceforge.net/samtools.shtml)
      Parameters:
      genomeName - : Genome's name (version)
      faidxFile - : FAI file used to create all chromosomes
      Returns:

    • add

      public void add(Chromosome chromo)
      Add a chromosome

    • chromosomeNamesSorted

      public List<String> chromosomeNamesSorted()
      Get a sorted list of chromosomes

    • getChromoFastaFiles

      public String[] getChromoFastaFiles()

    • getChromosome

      public Chromosome getChromosome(String chromoName)
      Find chromosome 'chromoName'

    • getChromosomeCount

      public int getChromosomeCount()

    • getChromosomes

      public Collection<Chromosome> getChromosomes()

    • getChromosomesSortedSize

      public List<Chromosome> getChromosomesSortedSize()
      Return chromosomes sorted by size (largest chromosomes first)

    • getCytoBands

      public CytoBands getCytoBands()

    • getGenes

      public Genes getGenes()

    • getGenesSorted

      public List<Gene> getGenesSorted()
      Create a sorted list of genes (sorted by gene Id)

    • getGenesSortedPos

      public List<Gene> getGenesSortedPos()
      Create a sorted list of genes (sorted by genomic position)

    • getGenomeId

      public String getGenomeId()

    • getGenomicSequences

      public GenomicSequences getGenomicSequences()

    • getOrCreateChromosome

      public Chromosome getOrCreateChromosome(String chromoName)
      Get or create a chromosome

    • getSpecies

      public String getSpecies()

    • getVersion

      public String getVersion()

    • hasChromosome

      public boolean hasChromosome(String chromo)
      Is this chromosome in this genome?

    • hasCodingInfo

      public boolean hasCodingInfo()

    • hasTranscriptSupportLevelInfo

      public boolean hasTranscriptSupportLevelInfo()
      Do we have coding info from genes?

    • isMostExonsHaveSequence

      public boolean isMostExonsHaveSequence()
      Do most exons have sequence? This is an indicator that something went really bad building the database.
      Returns:
      Check if most exons have sequence assigned.

    • iterator

      public Iterator<Chromosome> iterator()
      Specified by:
      iterator in interface Iterable<Chromosome>

    • length

      public long length()
      Total genome length: add all chromosomes

    • readGenomeSequence

      public boolean readGenomeSequence(String fastaFile)
      Read the whole genome sequence into memory
      Parameters:
      fastaFile - : Path to a Fasta file
      Returns:
      true if it was successful

    • remove

      public void remove(Chromosome chromo)
      Remove a chromosome WARINIG: Doesn't check any dependencies!

    • save

      public void save(String fileName)
      Save genome to file

    • serializeParse

      public void serializeParse(MarkerSerializer markerSerializer)
      Parse a line from a serialized file
      Specified by:
      serializeParse in interface TxtSerializable
      Overrides:
      serializeParse in class Marker

    • serializeSave

      public String serializeSave(MarkerSerializer markerSerializer)
      Create a string to serialize to a file
      Specified by:
      serializeSave in interface TxtSerializable
      Overrides:
      serializeSave in class Marker

    • toString

      public String toString()
      Show number of genes, transcripts & exons
      Overrides:
      toString in class Marker

    • toString

      public String toString(StringBuilder errors)
      Show number of genes, transcripts & exons Arr all errors to buffer