Class: BioVcf::VcfRecord

Inherits:
Object
  • Object
show all
Includes:
VcfRecordCall
Defined in:
lib/bio-vcf/vcfrecord.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from VcfRecordCall

#call_diff, #call_normal_count, #call_nuc, #call_tumor_count, #call_tumor_relative_count, #get_gt, #index

Constructor Details

#initialize(fields, header) ⇒ VcfRecord

Returns a new instance of VcfRecord.



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# File 'lib/bio-vcf/vcfrecord.rb', line 129

def initialize fields, header
  @fields = fields
  @header = header
  @sample_by_index = []
end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(m, *args, &block) ⇒ Object

Return the sample



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# File 'lib/bio-vcf/vcfrecord.rb', line 312

def method_missing(m, *args, &block)  
  name = m.to_s
  if name =~ /\?$/
    # Query for empty sample name
    @sample_index ||= @header.sample_index
    return !VcfSample::empty?(@fields[@sample_index[name.chop]])
  else
    sample[name]
  end
end

Instance Attribute Details

#header ⇒ Object (readonly)

Returns the value of attribute header.



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# File 'lib/bio-vcf/vcfrecord.rb', line 127

def header
  @header
end

Instance Method Details

#add_to_filter_field(str) ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 296

def add_to_filter_field str
  filter = @fields[6]
  if not filter or filter == '.' or filter == 'PASS'
    filter = str
  else
    values = filter.split(/;/)
    if not values.include?(str)
      filter = filter +';'+str
    end
  end
  filter = '.' if filter == nil or filter == ''
  @fields[6] = filter
  filter
end

#alt ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 157

def alt
  @alt ||= @fields[4].split(/,/)
end

#chrom ⇒ Object Also known as: chr 



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# File 'lib/bio-vcf/vcfrecord.rb', line 135

def chrom
  @fields[0]
end

#each_sample(list = nil) ⇒ Object

Walk the samples. list contains an Array of int (the index)



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# File 'lib/bio-vcf/vcfrecord.rb', line 208

def each_sample(list = nil)
  list = @header.samples_index_array() if not list 
  list.each { |i| yield VcfSample::Sample.new(self,sample_by_index(i.to_i)) }
end

#eval(expr, ignore_missing_data: true, quiet: false) ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 230

def eval expr, ignore_missing_data: true, quiet: false
  begin
    if not respond_to?(:call_cached_eval)
      code =
      """
      def call_cached_eval(rec,fields)
        r = rec
        #{expr}
      end
      """
      self.class.class_eval(code)
    end
    res = call_cached_eval(self,@fields)
    if res.kind_of?(Array)
      res.join("\t")
    else
      res
    end
  rescue NoMethodError => e
    if not quiet
      $stderr.print "RECORD ERROR!\n"
      $stderr.print [@fields],"\n"
      $stderr.print expr,"\n"
    end
    if ignore_missing_data
      $stderr.print e.message if not quiet
      return false
    else
      raise
    end
  end
end

#filter ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 165

def filter
  @filter ||= @fields[6]
end

#first ⇒ Object

Return the first (single) sample (used in one sample VCF)



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# File 'lib/bio-vcf/vcfrecord.rb', line 178

def first
  @first ||= VcfGenotypeField.new(@fields[9],format,@header,ref,alt)
end

#format ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 173

def format
  @format ||= VcfRecordParser.get_format(@fields[8])
end

#gfilter(expr, ignore_missing_data: true, quiet: false) ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 263

def gfilter expr, ignore_missing_data: true, quiet: false
  begin
    if not respond_to?(:call_cached_filter)
      code =
      """
      def call_cached_gfilter(rec,fields)
        r = rec
        #{expr}
      end
      """
      self.class.class_eval(code)
    end
    res = call_cached_gfilter(self,@fields)
    if res.kind_of?(Array)
      res.join("\t")
    else
      res
    end
  rescue NoMethodError => e
    if not quiet
      $stderr.print "RECORD ERROR!\n"
      $stderr.print [@fields],"\n"
      $stderr.print expr,"\n"
    end
    if ignore_missing_data
      $stderr.print e.message if not quiet
      return false
    else
      raise
    end
  end
end

#id ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 149

def id
  ids[0]
end

#ids ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 145

def ids 
  @ids ||= @fields[2].split(';')
end

#info ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 169

def info
  @info ||= VcfRecordParser.get_info(@fields[7])
end

#missing_samples? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio-vcf/vcfrecord.rb', line 219

def missing_samples?
  @fields[9..-1].each { |sample|
    return true if VcfSample::empty?(sample)
  }
  false
end

#normal ⇒ Object

Return the normal sample (used in two sample VCF)



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# File 'lib/bio-vcf/vcfrecord.rb', line 183

def normal
  first
end

#pos ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 141

def pos
  @pos ||= @fields[1].to_i
end

#qual ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 161

def qual
  @qual ||= @fields[5].to_f
end

#ref ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 153

def ref
  @refs ||= @fields[3]
end

#sample ⇒ Object

Return the sample as a named hash



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# File 'lib/bio-vcf/vcfrecord.rb', line 193

def sample 
  @sample ||= VcfGenotypeFields.new(@fields,format,@header,ref,alt)
end

#sample_by_index(i) ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 201

def sample_by_index i
  # p @fields
  raise "Can not index sample on parameter <#{i}>" if not i.kind_of?(Integer)
  @sample_by_index[i] ||= VcfGenotypeField.new(@fields[i+9],format,@header,ref,alt)
end

#sample_by_name(name) ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 197

def sample_by_name name
  sample[name]
end

#samples ⇒ Object 



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# File 'lib/bio-vcf/vcfrecord.rb', line 213

def samples
  list = []
  each_sample { |s| list << s }
  list
end

#tumor ⇒ Object

Return the tumor sample (used in two sample VCF)



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# File 'lib/bio-vcf/vcfrecord.rb', line 188

def tumor
  @tumor ||= VcfGenotypeField.new(@fields[10],format,@header,ref,alt)
end

#valid? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio-vcf/vcfrecord.rb', line 226

def valid?
  @fields.size == @header.column_names.size
end