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(bcf_t, header) ⇒ Record

Returns a new instance of Record.



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

def initialize(bcf_t, header)
  @bcf1 = bcf_t
  @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 11

def header
  @header
end

Instance Method Details

#alleles ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 86

def alleles
  LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_STR)
  @bcf1[:d][:allele].get_array_of_pointer(
    0, @bcf1[:n_allele]
  ).map(&:read_string)
end

#alt ⇒ Object 



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

def alt
  LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_STR)
  @bcf1[:d][:allele].get_array_of_pointer(
    FFI::TYPE_POINTER.size, @bcf1[:n_allele] - 1
  ).map(&:read_string)
end

#chrom ⇒ Object 



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

def chrom
  rid = @bcf1[:rid]

  LibHTS.bcf_hdr_id2name(@header.struct, rid)
end

#filter ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 50

def filter
  LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_FLT)
  d = @bcf1[:d]
  n_flt = d[:n_flt]

  case n_flt
  when 0
    "PASS"
  when 1
    i = d[:flt].read_int
    LibHTS.bcf_hdr_int2id(@header.struct, LibHTS::BCF_DT_ID, i)
  when 2
    d[:flt].get_array_of_int(0, n_flt).map do |i|
      LibHTS.bcf_hdr_int2id(@header.struct, LibHTS::BCF_DT_ID, i)
    end
  else
    raise "Unexpected number of filters. n_flt: #{n_flt}"
  end
end

#format ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 98

def format
  LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_FMT)
  Format.new(self)
end

#formats ⇒ Object

def inspect; end



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# File 'lib/hts/bcf/record.rb', line 23

def formats; end

#genotypes ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 25

def genotypes; end

#id ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 45

def id
  LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_INFO)
  @bcf1[:d][:id]
end

#info ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 93

def info
  LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_SHR)
  Info.new(self)
end

#pos ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 33

def pos
  @bcf1[:pos] + 1 # FIXME
end

#qual ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 70

def qual
  @bcf1[:qual]
end

#ref ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 74

def ref
  LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_STR)
  @bcf1[:d][:allele].get_pointer(0).read_string
end

#start ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 37

def start
  @bcf1[:pos]
end

#stop ⇒ Object 



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

def stop
  @bcf1[:pos] + @bcf1[:rlen]
end

#struct ⇒ Object 



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

def struct
  @bcf1
end

#to_ptr ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 17

def to_ptr
  @bcf1.to_ptr
end

#to_s ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 103

def to_s
  ksr = LibHTS::KString.new
  raise "Failed to format record" if LibHTS.vcf_format(@header.struct, @bcf1, ksr) == -1

  ksr[:s]
end