Class: HTS::Bcf::Record

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

Overview

A class for working with VCF records.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(header, bcf_t = nil) ⇒ Record

Returns a new instance of Record.



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# File 'lib/hts/bcf/record.rb', line 7

def initialize(header, bcf_t = nil)
  @bcf1 = bcf_t || LibHTS.bcf_init
  @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 12

def header
  @header
end

Instance Method Details

#alleles ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 76

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 69

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

Get the chromosome of variant.



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# File 'lib/hts/bcf/record.rb', line 32

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

#clear_id ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 60

def clear_id
  LibHTS.bcf_update_id(@header, @bcf1, ".")
end

#endpos ⇒ Object

Return the 0-based, exclusive end position



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# File 'lib/hts/bcf/record.rb', line 46

def endpos
  pos + @bcf1[:rlen]
end

#filter ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 92

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
    id = d[:flt].read_int
    LibHTS.bcf_hdr_int2id(@header.struct, LibHTS::BCF_DT_ID, id)
  when 2..nil
    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(key = nil) ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 122

def format(key = nil)
  LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_FMT)
  if key
    Format.new(self).get(key)
  else
    Format.new(self)
  end
end

#id ⇒ Object

Return the value of the ID column.



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# File 'lib/hts/bcf/record.rb', line 51

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

#id=(id) ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 56

def id=(id)
  LibHTS.bcf_update_id(@header, @bcf1, id)
end

#info(key = nil) ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 112

def info(key = nil)
  LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_SHR)
  info = Info.new(self)
  if key
    info.get(key)
  else
    info
  end
end

#pos ⇒ Object

Return 0-based position.



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

def pos
  @bcf1[:pos]
end

#pos=(pos) ⇒ Object 



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

def pos=(pos)
  @bcf1[:pos] = pos
end

#qual ⇒ Object

Get variant quality.



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# File 'lib/hts/bcf/record.rb', line 84

def qual
  @bcf1[:qual]
end

#qual=(qual) ⇒ Object 



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

def qual=(qual)
  @bcf1[:qual] = qual
end

#ref ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 64

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

#rid ⇒ Object

Get the reference id of the record.



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

def rid
  @bcf1[:rid]
end

#rid=(rid) ⇒ Object 



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

def rid=(rid)
  @bcf1[:rid] = rid
end

#struct ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 14

def struct
  @bcf1
end

#to_ptr ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 18

def to_ptr
  @bcf1.to_ptr
end

#to_s ⇒ Object 



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# File 'lib/hts/bcf/record.rb', line 131

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

  ksr[:s]
end