Class: HTS::Bcf::Record

Inherits:
Object
  • Object
show all
Defined in:
lib/hts/bcf/record.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(header, native_record = nil) ⇒ Record

Returns a new instance of Record.



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# File 'lib/hts/bcf/record.rb', line 8

def initialize(header, native_record = nil)
  @native = native_record || Native::BcfRecordHandle.create
  @header = header
end

Instance Attribute Details

#header ⇒ Object (readonly)

Returns the value of attribute header.



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# File 'lib/hts/bcf/record.rb', line 6

def header
  @header
end

Instance Method Details

#allele_count ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 42

def allele_count = alleles.length

#alleles ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 39

def alleles = @native.alleles

#alleles=(values) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/hts/bcf/record.rb', line 44

def alleles=(values)
  values = Array(values).map(&:to_s)
  raise ArgumentError, "at least one allele is required" if values.empty?

  encoded = values.join(",")
  check_update_rc!(@native.set_alleles(@header.__send__(:native_handle), encoded), "alleles", encoded)
  values
end

#alt ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 41

def alt = alleles.drop(1)

#chrom ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 19

def chrom = @header.id2name(rid)

#clear_id ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 34

def clear_id
  check_update_rc!(@native.set_id(@header.__send__(:native_handle), "."), "ID", ".")
  nil
end

#each_allele_raw ⇒ Object

Native migration replacement for the former pointer-yielding API.



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# File 'lib/hts/bcf/record.rb', line 54

def each_allele_raw
  return to_enum(__method__) unless block_given?

  alleles.each { |allele| yield allele, allele.bytesize }
  self
end

#each_filter_id(&block) ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 81

def each_filter_id(&block)
  return to_enum(__method__) unless block_given?

  @native.filter_ids.each(&block)
  self
end

#endpos ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 26

def endpos = pos + @native.core_get(:rlen)

#filter_id?(target_id) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bcf/record.rb', line 89

def filter_id?(target_id) = filter_ids.include?(Integer(target_id))

#filter_ids ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 88

def filter_ids = @native.filter_ids

#filter_missing? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bcf/record.rb', line 78

def filter_missing? = filters.empty?

#filtered? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bcf/record.rb', line 79

def filtered? = !passed? && !filter_missing?

#filters ⇒ Object Also known as: filter 



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# File 'lib/hts/bcf/record.rb', line 67

def filters
  names = @native.filter_names(@header.__send__(:native_handle))
  names
end

#format(key = nil) ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 96

def format(key = nil)
  accessor = (@format_accessor ||= Format.new(self))
  key ? accessor.get(key) : accessor
end

#id ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 27

def id = @native.id

#id=(value) ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 29

def id=(value)
  check_update_rc!(@native.set_id(@header.__send__(:native_handle), value), "ID", value)
  value
end

#info(key = nil) ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 91

def info(key = nil)
  accessor = (@info_accessor ||= Info.new(self))
  key ? accessor.get(key) : accessor
end

#passed? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bcf/record.rb', line 77

def passed? = filters == ["PASS"]

#pos ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 20

def pos = @native.core_get(:pos)

#pos=(value) ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 22

def pos=(value)
  @native.core_set(:pos, value)
end

#qual ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 61

def qual = @native.core_get(:qual)

#qual=(value) ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 63

def qual=(value)
  @native.core_set(:qual, value)
end

#ref ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 40

def ref = alleles.first

#rid ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 13

def rid = @native.core_get(:rid)

#rid=(value) ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 15

def rid=(value)
  @native.core_set(:rid, value)
end

#to_s ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 101

def to_s = @native.format_record(@header.__send__(:native_handle))