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 



49
50
51
 
# 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:



56
57
58
59
60
61
62
63
64
65
66
67
68
69
 
# 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



134
135
136
 
# File 'lib/exodb/datamodel/variant.rb', line 134

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