Class: BioInterchange::Genomics::VCFFeature

Inherits:
GFF3Feature
  • Object
show all
Defined in:
lib/biointerchange/genomics/vcf_feature.rb

Overview

Represents a single genomic feature of a VCF file.

Constant Summary

Constants inherited from GFF3Feature

GFF3Feature::NEGATIVE, GFF3Feature::NOT_STRANDED, GFF3Feature::POSITIVE, GFF3Feature::UNKNOWN

Instance Method Summary collapse

Methods inherited from GFF3Feature

#attributes, #end_coordinate, #phase, #score, #sequence_id, #source, #start_coordinate, #strand, #type

Constructor Details

#initialize(chromosome, position, id, reference_bases, alternative_alleles, quality_score, filters, info = {}, samples = []) ⇒ VCFFeature

Creates a new feature representation. A feature is described on one line of the VCF file.

chromosome

an identifier that determines the chromosome on which the feature resides

position

the feature locus on the chromosome

id

a unique identifier of the feature

reference_bases

reference alleles of the feature

alternative_alleles

alternative alleles of the feature (non-reference alleles)

quality_score

phred-scaled quality score for the assertions concerning reference-/alternative-alleles

filters

list of VCF filters that a feature has failed

info

a map of additional attributes associated with the feature

samples

sample information specific to the described feature



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# File 'lib/biointerchange/genomics/vcf_feature.rb', line 17

def initialize(chromosome, position, id, reference_bases, alternative_alleles, quality_score, filters, info = {}, samples = [])
  # Fill in phase, which is always omitted in GVF features (after 'strand', before 'attributes'):
  # Translations to somewhat fit the existing GFF3/GVF model (GFF3/GVF left, VCF right):
  #
  #   sequence_id -> chromosome
  #   source -> nil
  #   type -> nil
  #   start_coordinate -> position
  #   end_coordinate -> position
  #   score -> quality_score
  #   strand -> nil
  #   phase -> nil
  #   attributes -> info
  #
  # Parameters that do not map directly to super's parameters are placed in `info`
  # with a space as prefix. For example, `reference_bases` becomes the key
  # ` reference_bases` in `info`.
  info[' id'] = [ id ] if id
  info[' reference_bases'] = [ reference_bases ]
  info[' alternative_alleles'] = alternative_alleles
  info[' filters'] = filters
  info[' samples'] = samples

  super(chromosome, nil, nil, position, position, quality_score, BioInterchange::Genomics::GFF3Feature::POSITIVE, nil, info)
end