Class GenomicSequences

java.lang.Object
org.snpeff.binseq.GenomicSequences
All Implemented Interfaces:
Serializable, Iterable<MarkerSeq>

public class GenomicSequences extends Object implements Iterable<MarkerSeq>, Serializable
This class stores all "relevant" sequences in a genome This class is able to: i) Add all regions of interest ii) Store genomic sequences for those regions of interest iii) Retrieve genomic sequences by interval
Author:
pcingola
See Also:
  • Field Details

  • Constructor Details

    • GenomicSequences

      public GenomicSequences(Genome genome)
  • Method Details

    • addChromosomeSequence

      public void addChromosomeSequence(String chr, String chrSeq)
      Create a sequence for the whole chromsome (mostly used in test cases)
    • addGeneSequences

      public int addGeneSequences(String chr, String chrSeq)
      Add sequences for each gene in the genome
    • build

      public void build()
      Build interval forest
    • clear

      public void clear()
    • hasChromosome

      public boolean hasChromosome(String chr)
      Do we have sequence information for this chromosome?
    • isEmpty

      public boolean isEmpty()
    • iterator

      public Iterator<MarkerSeq> iterator()
      Specified by:
      iterator in interface Iterable<MarkerSeq>
    • load

      public boolean load()
      Load sequences for all 'small chromosomes" (from "sequence.bin" file)
    • load

      public boolean load(String chr)
      Load sequences for a single chromosome (from "sequence.chr.bin" file)
    • loadOrCreateFromGenome

      public boolean loadOrCreateFromGenome(String chr)
      Load sequences from genomic sequence file or (if not file is available) generate some sequences from exons.
    • queryMarkerSequence

      public MarkerSeq queryMarkerSequence(Marker marker)
      Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form database
      Returns:
      A markerSeq containing 'marker' or null if nothing is found
    • querySequence

      public String querySequence(Marker marker)
      Get sequence for a marker
    • reset

      public void reset()
    • save

      public void save(Config config)
      Save genomic sequence into separate files (per chromosome)
    • setDisableLoad

      public void setDisableLoad(boolean disableLoad)
    • setVerbose

      public void setVerbose(boolean verbose)
    • toString

      public String toString()
      Overrides:
      toString in class Object