Class: Exodb::Variant

Inherits:
Object
  • Object
show all
Includes:
GenomeLocationField, Mongoid::Document, Mongoid::Timestamps, Mongoid::Versioning
Defined in:
lib/exodb/datamodel/variant.rb

Direct Known Subclasses

CNV, Indel, SNV

Class Method Summary collapse

Instance Method Summary collapse

Methods included from GenomeLocationField

#begin, #chromosome, #end, #location_str, #parse_location, #start, #stop

Class Method Details

.from_pileup(pileupline) ⇒ Object 



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# File 'lib/exodb/datamodel/variant.rb', line 49

def self.from_pileup(pileupline)
	
end

Instance Method Details

#add_to_sample(str) ⇒ Object Also known as: add_to_cell

add this variant to original cell sample

Parameters:



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# File 'lib/exodb/datamodel/variant.rb', line 56

def add_to_sample(str)
	
	sample = Cell.where({'oid' => str})
	
	if sample.exists?
		self.cell = sample.first()
		#output.puts "#EXODB:INFO This sample is added to #{dataset.first().name}." if $0 == 'pry'
	else
		#output.puts "#EXODB:ERRO Cannot find dataset by #{str}." if $0 == 'pry'
	end
	
	self.oid = "#{self.location_str}:#{sample.first().oid}"
	
end

#apply_filter(filter) ⇒ Object

apply filter to the variant the result is kelp in passfilter

Parameters:

  • pile-up (String) —

    line from mpileup



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# File 'lib/exodb/datamodel/variant.rb', line 134

def apply_filter(filter)
	self[:filter] = filter
end