Module: EnsemblREST::GA4GH

Defined in:
lib/ensemblrest/variationga4gh.rb

Class Method Summary collapse

Class Method Details

.gacallSet(options = {}) ⇒ JSON

Return a list of sets of genotype calls for specific samples in GA4GH format

Parameters:

Returns:

  • (JSON) —

    a list of sets of genotype calls for specific samples



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# File 'lib/ensemblrest/variationga4gh.rb', line 21

def gacallSet(options = {})
  return EnsemblREST.post("ga4gh/callsets/search", {}, {format: 'json'}.merge(options))
end

.gavariants(start, stop, referenceName, variantSetIds, options = {}) ⇒ JSON

Return variant call information in GA4GH format for a region on a reference sequence

Parameters:

  • start (Integer) —

    Start position of region (zero-based, inclusive)

  • stop (Integer) —

    End position of region (zero-based, exclusive)

  • referenceName (String) —

    Reference sequence name

  • variantSetIds (Array) —

    Return variant data for specific variantSets

  • options (Hash) (defaults to: {}) —

    Optional arguments for the service please goto rest.ensembl.org/documentation/info/gavariants

Returns:

  • (JSON) —

    variant call information in GA4GH format



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# File 'lib/ensemblrest/variationga4gh.rb', line 33

def gavariants(start, stop, referenceName, variantSetIds, options = {})
  return EnsemblREST.post("ga4gh/variants/search", {"variantSetIds" => variantSetIds, "referenceName" => referenceName,"start" => start ,"end" => stop}, {format: 'json'}.merge(options))
end

.gavariantset(options = {}) ⇒ JSON

Return a list of variant sets in GA4GH format

Parameters:

Returns:

  • (JSON) —

    a list of variant sets in GA4GH format



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# File 'lib/ensemblrest/variationga4gh.rb', line 41

def gavariantset(options = {})
  return EnsemblREST.post("ga4gh/variantsets/search", {}, {format: 'json'}.merge(options))
end