Module: BioVcf::VcfHeaderParser::RagelKeyValues

Defined in:
lib/bio-vcf/vcfheader_line.rb

Class Attribute Summary collapse

Class Method Summary collapse

Class Attribute Details

._simple_lexer_actions ⇒ Object

Returns the value of attribute _simple_lexer_actions.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 39

def _simple_lexer_actions
  @_simple_lexer_actions
end

._simple_lexer_eof_actions ⇒ Object

Returns the value of attribute _simple_lexer_eof_actions.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 422

def _simple_lexer_eof_actions
  @_simple_lexer_eof_actions
end

._simple_lexer_index_offsets ⇒ Object

Returns the value of attribute _simple_lexer_index_offsets.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 220

def _simple_lexer_index_offsets
  @_simple_lexer_index_offsets
end

._simple_lexer_key_offsets ⇒ Object

Returns the value of attribute _simple_lexer_key_offsets.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 53

def _simple_lexer_key_offsets
  @_simple_lexer_key_offsets
end

._simple_lexer_range_lengths ⇒ Object

Returns the value of attribute _simple_lexer_range_lengths.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 196

def _simple_lexer_range_lengths
  @_simple_lexer_range_lengths
end

._simple_lexer_single_lengths ⇒ Object

Returns the value of attribute _simple_lexer_single_lengths.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 172

def _simple_lexer_single_lengths
  @_simple_lexer_single_lengths
end

._simple_lexer_trans_actions ⇒ Object

Returns the value of attribute _simple_lexer_trans_actions.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 333

def _simple_lexer_trans_actions
  @_simple_lexer_trans_actions
end

._simple_lexer_trans_keys ⇒ Object

Returns the value of attribute _simple_lexer_trans_keys.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 77

def _simple_lexer_trans_keys
  @_simple_lexer_trans_keys
end

._simple_lexer_trans_targs ⇒ Object

Returns the value of attribute _simple_lexer_trans_targs.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 244

def _simple_lexer_trans_targs
  @_simple_lexer_trans_targs
end

.simple_lexer_en_main ⇒ Object

Returns the value of attribute simple_lexer_en_main.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 459

def simple_lexer_en_main
  @simple_lexer_en_main
end

.simple_lexer_error ⇒ Object

Returns the value of attribute simple_lexer_error.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 454

def simple_lexer_error
  @simple_lexer_error
end

.simple_lexer_first_final ⇒ Object

Returns the value of attribute simple_lexer_first_final.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 450

def simple_lexer_first_final
  @simple_lexer_first_final
end

.simple_lexer_start ⇒ Object

Returns the value of attribute simple_lexer_start.



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# File 'lib/bio-vcf/vcfheader_line.rb', line 446

def simple_lexer_start
  @simple_lexer_start
end

Class Method Details

.debug(msg) ⇒ Object 



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# File 'lib/bio-vcf/vcfheader_line.rb', line 25

def self.debug msg
  # nothing
	# $stderr.print "DEBUG: ",msg,"\n"
end

.run_lexer(buf, options = {}) ⇒ Object

line 79 “gen_vcfheaderline_parser.rl” %% this just fixes syntax highlighting…



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# File 'lib/bio-vcf/vcfheader_line.rb', line 467

def self.run_lexer(buf, options = {})
  do_debug = (options[:debug] == true)
  $stderr.print "---> ",buf,"\n" if do_debug
  data = buf.unpack("c*") if(buf.is_a?(String))
  eof = data.length
  values = []
  stack = []

  emit = lambda { |type, data, ts, p|
    # Print the type and text of the last read token
    # p ts,p
    $stderr.print "EMITTED: #{type}: #{data[ts...p].pack('c*')}\n" if do_debug
    values << [type,data[ts...p].pack('c*')]
  }

  error_code = nil
  
  
# line 486 "gen_vcfheaderline_parser.rb"
begin
	p ||= 0
	pe ||= data.length
	cs = simple_lexer_start
end

# line 99 "gen_vcfheaderline_parser.rl"
  
# line 495 "gen_vcfheaderline_parser.rb"
begin
	_klen, _trans, _keys, _acts, _nacts = nil
	_goto_level = 0
	_resume = 10
	_eof_trans = 15
	_again = 20
	_test_eof = 30
	_out = 40
	while true
	_trigger_goto = false
	if _goto_level <= 0
	if p == pe
		_goto_level = _test_eof
		next
	end
	if cs == 0
		_goto_level = _out
		next
	end
	end
	if _goto_level <= _resume
	_keys = _simple_lexer_key_offsets[cs]
	_trans = _simple_lexer_index_offsets[cs]
	_klen = _simple_lexer_single_lengths[cs]
	_break_match = false
	
	begin
	  if _klen > 0
	     _lower = _keys
	     _upper = _keys + _klen - 1

	     loop do
	        break if _upper < _lower
	        _mid = _lower + ( (_upper - _lower) >> 1 )

	        if data[p].ord < _simple_lexer_trans_keys[_mid]
	           _upper = _mid - 1
	        elsif data[p].ord > _simple_lexer_trans_keys[_mid]
	           _lower = _mid + 1
	        else
	           _trans += (_mid - _keys)
	           _break_match = true
	           break
	        end
	     end # loop
	     break if _break_match
	     _keys += _klen
	     _trans += _klen
	  end
	  _klen = _simple_lexer_range_lengths[cs]
	  if _klen > 0
	     _lower = _keys
	     _upper = _keys + (_klen << 1) - 2
	     loop do
	        break if _upper < _lower
	        _mid = _lower + (((_upper-_lower) >> 1) & ~1)
	        if data[p].ord < _simple_lexer_trans_keys[_mid]
	          _upper = _mid - 2
	        elsif data[p].ord > _simple_lexer_trans_keys[_mid+1]
	          _lower = _mid + 2
	        else
	          _trans += ((_mid - _keys) >> 1)
	          _break_match = true
	          break
	        end
	     end # loop
	     break if _break_match
	     _trans += _klen
	  end
	end while false
	cs = _simple_lexer_trans_targs[_trans]
	if _simple_lexer_trans_actions[_trans] != 0
		_acts = _simple_lexer_trans_actions[_trans]
		_nacts = _simple_lexer_actions[_acts]
		_acts += 1
		while _nacts > 0
			_nacts -= 1
			_acts += 1
			case _simple_lexer_actions[_acts - 1]
when 0 then
# line 33 "gen_vcfheaderline_parser.rl"
		begin
 ts=p 		end
when 1 then
# line 34 "gen_vcfheaderline_parser.rl"
		begin

    emit.call(:value,data,ts,p)
  		end
when 2 then
# line 38 "gen_vcfheaderline_parser.rl"
		begin

    emit.call(:kw,data,ts,p)
  		end
when 3 then
# line 58 "gen_vcfheaderline_parser.rl"
		begin
 emit.call(:key_word,data,ts,p) 		end
when 4 then
# line 59 "gen_vcfheaderline_parser.rl"
		begin
 emit.call(:value,data,ts,p) 		end
when 5 then
# line 60 "gen_vcfheaderline_parser.rl"
		begin
 emit.call(:value,data,ts,p) 		end
when 6 then
# line 62 "gen_vcfheaderline_parser.rl"
		begin
 emit.call(:value,data,ts,p) 		end
when 7 then
# line 65 "gen_vcfheaderline_parser.rl"
		begin
 emit.call(:value,data,ts,p) 		end
when 8 then
# line 67 "gen_vcfheaderline_parser.rl"
		begin
 debug("ID FOUND") 		end
when 9 then
# line 67 "gen_vcfheaderline_parser.rl"
		begin
 error_code="Malformed ID"		end
when 10 then
# line 68 "gen_vcfheaderline_parser.rl"
		begin
 error_code="Version"		end
when 11 then
# line 69 "gen_vcfheaderline_parser.rl"
		begin
 error_code="Number"		end
when 12 then
# line 70 "gen_vcfheaderline_parser.rl"
		begin
 debug("DATE FOUND") 		end
when 13 then
# line 70 "gen_vcfheaderline_parser.rl"
		begin
 error_code="Date"		end
when 14 then
# line 71 "gen_vcfheaderline_parser.rl"
		begin
 error_code="GATK"		end
when 15 then
# line 72 "gen_vcfheaderline_parser.rl"
		begin
 debug("KEY_VALUE found") 		end
when 16 then
# line 72 "gen_vcfheaderline_parser.rl"
		begin
 error_code="unknown key-value " 		end
# line 647 "gen_vcfheaderline_parser.rb"
			end # action switch
		end
	end
	if _trigger_goto
		next
	end
	end
	if _goto_level <= _again
	if cs == 0
		_goto_level = _out
		next
	end
	p += 1
	if p != pe
		_goto_level = _resume
		next
	end
	end
	if _goto_level <= _test_eof
	if p == eof
	__acts = _simple_lexer_eof_actions[cs]
	__nacts =  _simple_lexer_actions[__acts]
	__acts += 1
	while __nacts > 0
		__nacts -= 1
		__acts += 1
		case _simple_lexer_actions[__acts - 1]
when 9 then
# line 67 "gen_vcfheaderline_parser.rl"
		begin
 error_code="Malformed ID"		end
when 10 then
# line 68 "gen_vcfheaderline_parser.rl"
		begin
 error_code="Version"		end
when 11 then
# line 69 "gen_vcfheaderline_parser.rl"
		begin
 error_code="Number"		end
when 13 then
# line 70 "gen_vcfheaderline_parser.rl"
		begin
 error_code="Date"		end
when 14 then
# line 71 "gen_vcfheaderline_parser.rl"
		begin
 error_code="GATK"		end
when 16 then
# line 72 "gen_vcfheaderline_parser.rl"
		begin
 error_code="unknown key-value " 		end
# line 699 "gen_vcfheaderline_parser.rb"
		end # eof action switch
	end
	if _trigger_goto
		next
	end
end
	end
	if _goto_level <= _out
		break
	end
	end
	end

# line 100 "gen_vcfheaderline_parser.rl"

  raise "ERROR: "+error_code+" in "+buf if error_code

  begin
    res = {}
    # p values
    values.each_slice(2) do | a,b |
      $stderr.print '*',a,b if do_debug
      keyword = a[1]
      value = b[1]
      value = value.to_i if ['length','Epoch'].index(keyword)
      res[keyword] = value
      # p h[:value] if h[:name]==:identifier or h[:name]==:value or h[:name]==:string
    end
  rescue
    print "ERROR: "
    p values
    raise
  end
  $stderr.print(res,"\n") if do_debug
  res
end