Class: CagnutPipelineDraw::Pipeline::VariantCall

Inherits:
Object
  • Object
show all
Defined in:
lib/cagnut_pipeline_draw/pipeline/variant_call.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(job_name) ⇒ VariantCall

Returns a new instance of VariantCall.



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# File 'lib/cagnut_pipeline_draw/pipeline/variant_call.rb', line 6

def initialize job_name
  @job_name = job_name
  @config = Cagnut::Configuration.config
  @gatk = ::CagnutGatk::Util.new @config
  @snpeff = ::CagnutSnpeff::Util.new
end

Instance Attribute Details

#gatk ⇒ Object

Returns the value of attribute gatk.



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# File 'lib/cagnut_pipeline_draw/pipeline/variant_call.rb', line 4

def gatk
  @gatk
end

#snp_eff ⇒ Object

Returns the value of attribute snp_eff.



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# File 'lib/cagnut_pipeline_draw/pipeline/variant_call.rb', line 4

def snp_eff
  @snp_eff
end

Instance Method Details

#run(filename = nil, order = 1) ⇒ Object 



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# File 'lib/cagnut_pipeline_draw/pipeline/variant_call.rb', line 13

def run filename = nil, order=1
  order = @gatk.depth_of_coverage gatk_depth_of_coverage_dirs, order, @job_name, filename
  job_name, filename, order = @gatk.unified_genotyper gatk_unified_genotyper_dirs, order, @job_name, filename
  job_name, filename, order = @gatk.snpcal gatk_snpcal_dirs, order, job_name, filename
  job_name, order = @snpeff.snp_annotation snpeff_snp_annotation_dirs, order, job_name, filename
  # collectSPeekMetrics
  [job_name, nil, order+1]
end