bio-vcf 0.8.2 → 0.9.0

metadata

@@ -1,71 +1,15 @@
 --- !ruby/object:Gem::Specification
 name: bio-vcf
 version: !ruby/object:Gem::Version
-  version: 0.8.2
+  version: 0.9.0
 platform: ruby
 authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-12-28 00:00:00.000000000 Z
-dependencies:
-- !ruby/object:Gem::Dependency
-  name: rspec
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 2.14.0
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 2.14.0
-- !ruby/object:Gem::Dependency
-  name: cucumber
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.3.11
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.3.11
-- !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 2.0.1
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 2.0.1
-- !ruby/object:Gem::Dependency
-  name: regressiontest
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.0.3
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.0.3
+date: 2015-08-16 00:00:00.000000000 Z
+dependencies: []
 description: Smart lazy multi-threaded parser for VCF format with useful filtering
   and output rewriting
 email: pjotr.public01@thebird.nl
@@ -78,10 +22,10 @@ extra_rdoc_files:
 files:
 - ".travis.yml"
 - Gemfile
-- Gemfile.lock
 - LICENSE.txt
 - README.md
 - Rakefile
+- TAGS
 - VERSION
 - bin/bio-vcf
 - bio-vcf.gemspec
@@ -101,6 +45,7 @@ files:
 - features/vcf_header.feature
 - lib/bio-vcf.rb
 - lib/bio-vcf/bedfilter.rb
+- lib/bio-vcf/pcows.rb
 - lib/bio-vcf/template.rb
 - lib/bio-vcf/utils.rb
 - lib/bio-vcf/variant.rb
@@ -113,7 +58,6 @@ files:
 - lib/bio-vcf/vcfrecord.rb
 - lib/bio-vcf/vcfsample.rb
 - lib/bio-vcf/vcfstatistics.rb
-- ragel/gen_vcfheaderline_parser.rb
 - ragel/gen_vcfheaderline_parser.rl
 - ragel/generate.sh
 - template/gatk_vcf2rdf.erb
@@ -123,20 +67,52 @@ files:
 - template/vcf2rdf.erb
 - template/vcf2rdf_header.erb
 - test/data/input/dbsnp.vcf
+- test/data/input/gatk_exome.vcf
+- test/data/input/gatk_wgs.vcf
 - test/data/input/multisample.vcf
 - test/data/input/somaticsniper.vcf
+- test/data/input/test.bed
+- test/data/regression/eval_once-stderr.new
+- test/data/regression/eval_once.new
+- test/data/regression/eval_once.ref
+- test/data/regression/eval_r.info.dp-stderr.new
+- test/data/regression/eval_r.info.dp.new
 - test/data/regression/eval_r.info.dp.ref
+- test/data/regression/ifilter_s.dp-stderr.new
+- test/data/regression/ifilter_s.dp.new
 - test/data/regression/ifilter_s.dp.ref
+- test/data/regression/r.info.dp-stderr.new
+- test/data/regression/r.info.dp.new
 - test/data/regression/r.info.dp.ref
+- test/data/regression/rewrite.info.sample-stderr.new
+- test/data/regression/rewrite.info.sample.new
 - test/data/regression/rewrite.info.sample.ref
+- test/data/regression/s.dp-stderr.new
+- test/data/regression/s.dp.new
 - test/data/regression/s.dp.ref
+- test/data/regression/seval_s.dp-stderr.new
+- test/data/regression/seval_s.dp.new
 - test/data/regression/seval_s.dp.ref
+- test/data/regression/sfilter_seval_s.dp-stderr.new
+- test/data/regression/sfilter_seval_s.dp.new
 - test/data/regression/sfilter_seval_s.dp.ref
+- test/data/regression/thread4-stderr.new
+- test/data/regression/thread4.new
 - test/data/regression/thread4.ref
+- test/data/regression/thread4_4-stderr.new
+- test/data/regression/thread4_4.new
 - test/data/regression/thread4_4.ref
+- test/data/regression/thread4_4_failed_filter-stderr.new
 - test/data/regression/thread4_4_failed_filter-stderr.ref
+- test/data/regression/thread4_4_failed_filter.new
+- test/data/regression/vcf2json_full_header-stderr.new
+- test/data/regression/vcf2json_full_header.new
 - test/data/regression/vcf2json_full_header.ref
+- test/data/regression/vcf2json_use_meta-stderr.new
+- test/data/regression/vcf2json_use_meta.new
+- test/data/regression/vcf2json_use_meta.ref
 - test/performance/metrics.md
+- test/tmp/test.vcf
 homepage: http://github.com/pjotrp/bioruby-vcf
 licenses:
 - MIT
@@ -157,7 +133,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 2.4.5
 signing_key: 
 specification_version: 4
 summary: Fast multi-threaded VCF parser

data/Gemfile.lock

@@ -1,81 +0,0 @@
-GEM
-  remote: http://rubygems.org/
-  specs:
-    addressable (2.3.5)
-    builder (3.2.2)
-    cucumber (1.3.11)
-      builder (>= 2.1.2)
-      diff-lcs (>= 1.1.3)
-      gherkin (~> 2.12)
-      multi_json (>= 1.7.5, < 2.0)
-      multi_test (>= 0.0.2)
-    descendants_tracker (0.0.3)
-    diff-lcs (1.2.5)
-    faraday (0.9.0)
-      multipart-post (>= 1.2, < 3)
-    gherkin (2.12.2)
-      multi_json (~> 1.3)
-    gherkin (2.12.2-java)
-      multi_json (~> 1.3)
-    git (1.2.6)
-    github_api (0.11.3)
-      addressable (~> 2.3)
-      descendants_tracker (~> 0.0.1)
-      faraday (~> 0.8, < 0.10)
-      hashie (>= 1.2)
-      multi_json (>= 1.7.5, < 2.0)
-      nokogiri (~> 1.6.0)
-      oauth2
-    hashie (2.0.5)
-    highline (1.6.21)
-    jeweler (2.0.1)
-      builder
-      bundler (>= 1.0)
-      git (>= 1.2.5)
-      github_api
-      highline (>= 1.6.15)
-      nokogiri (>= 1.5.10)
-      rake
-      rdoc
-    json (1.8.1)
-    json (1.8.1-java)
-    jwt (0.1.11)
-      multi_json (>= 1.5)
-    mini_portile (0.5.2)
-    multi_json (1.9.0)
-    multi_test (0.0.3)
-    multi_xml (0.5.5)
-    multipart-post (2.0.0)
-    nokogiri (1.6.1)
-      mini_portile (~> 0.5.0)
-    nokogiri (1.6.1-java)
-      mini_portile (~> 0.5.0)
-    oauth2 (0.9.3)
-      faraday (>= 0.8, < 0.10)
-      jwt (~> 0.1.8)
-      multi_json (~> 1.3)
-      multi_xml (~> 0.5)
-      rack (~> 1.2)
-    rack (1.5.2)
-    rake (10.1.1)
-    rdoc (4.1.1)
-      json (~> 1.4)
-    regressiontest (0.0.3)
-    rspec (2.14.1)
-      rspec-core (~> 2.14.0)
-      rspec-expectations (~> 2.14.0)
-      rspec-mocks (~> 2.14.0)
-    rspec-core (2.14.8)
-    rspec-expectations (2.14.5)
-      diff-lcs (>= 1.1.3, < 2.0)
-    rspec-mocks (2.14.6)
-
-PLATFORMS
-  java
-  ruby
-
-DEPENDENCIES
-  cucumber (>= 1.3.11)
-  jeweler (>= 2.0.1)
-  regressiontest (>= 0.0.3)
-  rspec (>= 2.14.0)

data/ragel/gen_vcfheaderline_parser.rb

@@ -1,483 +0,0 @@
-
-# line 1 "gen_vcfheaderline_parser.rl"
-# Ragel lexer for VCF-header
-#
-# This is a partial lexer for the VCF header format. Bio-vcf uses this
-# to generate meta information in (for example) JSON format. The
-# advantage of using a full state engine is that it allows for easy
-# parsing of key-value pairs with syntax checking and, for example,
-# escaped quotes in quoted string values. This edition validates ID and
-# Number fields only.
-#
-# Note the .rb version is generated from ./ragel/gen_vcfheaderline_parser.rl
-
-module BioVcf
-
-  module VcfHeaderParser
-
-    module RagelKeyValues
-  
-=begin
-
-# line 57 "gen_vcfheaderline_parser.rl"
-
-=end
-
-
-# line 28 "gen_vcfheaderline_parser.rb"
-class << self
-	attr_accessor :_simple_lexer_actions
-	private :_simple_lexer_actions, :_simple_lexer_actions=
-end
-self._simple_lexer_actions = [
-	0, 1, 0, 1, 1, 1, 2, 1, 
-	3, 1, 4, 1, 5, 1, 6, 1, 
-	9, 2, 0, 1, 2, 7, 9, 2, 
-	8, 9, 3, 7, 8, 9
-]
-
-class << self
-	attr_accessor :_simple_lexer_key_offsets
-	private :_simple_lexer_key_offsets, :_simple_lexer_key_offsets=
-end
-self._simple_lexer_key_offsets = [
-	0, 0, 1, 2, 5, 6, 7, 8, 
-	14, 20, 27, 32, 34, 36, 38, 40, 
-	40, 40, 42, 44, 50, 57, 64, 68, 
-	74, 81, 89, 97, 105, 113, 120, 128, 
-	130, 132, 133, 134, 135, 136, 137, 138, 
-	139, 140, 141, 142, 144, 160, 167, 172, 
-	176, 184, 192, 196
-]
-
-class << self
-	attr_accessor :_simple_lexer_trans_keys
-	private :_simple_lexer_trans_keys, :_simple_lexer_trans_keys=
-end
-self._simple_lexer_trans_keys = [
-	35, 35, 65, 70, 73, 76, 84, 61, 
-	73, 78, 65, 90, 97, 122, 48, 57, 
-	65, 90, 97, 122, 61, 48, 57, 65, 
-	90, 97, 122, 32, 34, 39, 9, 13, 
-	34, 92, 34, 92, 39, 92, 39, 92, 
-	48, 57, 48, 57, 48, 57, 65, 90, 
-	97, 122, 68, 48, 57, 65, 90, 97, 
-	122, 61, 48, 57, 65, 90, 97, 122, 
-	65, 90, 97, 122, 48, 57, 65, 90, 
-	97, 122, 117, 48, 57, 65, 90, 97, 
-	122, 61, 109, 48, 57, 65, 90, 97, 
-	122, 61, 98, 48, 57, 65, 90, 97, 
-	122, 61, 101, 48, 57, 65, 90, 97, 
-	122, 61, 114, 48, 57, 65, 90, 97, 
-	122, 61, 48, 57, 65, 90, 97, 122, 
-	43, 45, 46, 65, 71, 82, 48, 57, 
-	48, 57, 73, 79, 76, 84, 69, 82, 
-	82, 77, 65, 78, 70, 79, 44, 60, 
-	32, 34, 39, 44, 46, 60, 9, 13, 
-	43, 45, 48, 57, 65, 90, 97, 122, 
-	32, 34, 39, 44, 60, 9, 13, 44, 
-	46, 60, 48, 57, 44, 60, 48, 57, 
-	44, 60, 48, 57, 65, 90, 97, 122, 
-	44, 60, 48, 57, 65, 90, 97, 122, 
-	44, 60, 48, 57, 44, 60, 0
-]
-
-class << self
-	attr_accessor :_simple_lexer_single_lengths
-	private :_simple_lexer_single_lengths, :_simple_lexer_single_lengths=
-end
-self._simple_lexer_single_lengths = [
-	0, 1, 1, 3, 1, 1, 1, 2, 
-	0, 1, 3, 2, 2, 2, 2, 0, 
-	0, 0, 0, 0, 1, 1, 0, 0, 
-	1, 2, 2, 2, 2, 1, 6, 0, 
-	2, 1, 1, 1, 1, 1, 1, 1, 
-	1, 1, 1, 2, 6, 5, 3, 2, 
-	2, 2, 2, 2
-]
-
-class << self
-	attr_accessor :_simple_lexer_range_lengths
-	private :_simple_lexer_range_lengths, :_simple_lexer_range_lengths=
-end
-self._simple_lexer_range_lengths = [
-	0, 0, 0, 0, 0, 0, 0, 2, 
-	3, 3, 1, 0, 0, 0, 0, 0, 
-	0, 1, 1, 3, 3, 3, 2, 3, 
-	3, 3, 3, 3, 3, 3, 1, 1, 
-	0, 0, 0, 0, 0, 0, 0, 0, 
-	0, 0, 0, 0, 5, 1, 1, 1, 
-	3, 3, 1, 0
-]
-
-class << self
-	attr_accessor :_simple_lexer_index_offsets
-	private :_simple_lexer_index_offsets, :_simple_lexer_index_offsets=
-end
-self._simple_lexer_index_offsets = [
-	0, 0, 2, 4, 8, 10, 12, 14, 
-	19, 23, 28, 33, 36, 39, 42, 45, 
-	46, 47, 49, 51, 55, 60, 65, 68, 
-	72, 77, 83, 89, 95, 101, 106, 114, 
-	116, 119, 121, 123, 125, 127, 129, 131, 
-	133, 135, 137, 139, 142, 154, 161, 166, 
-	170, 176, 182, 186
-]
-
-class << self
-	attr_accessor :_simple_lexer_indicies
-	private :_simple_lexer_indicies, :_simple_lexer_indicies=
-end
-self._simple_lexer_indicies = [
-	0, 1, 2, 1, 3, 4, 5, 1, 
-	6, 1, 7, 1, 8, 1, 11, 12, 
-	10, 10, 9, 14, 14, 14, 13, 15, 
-	14, 14, 14, 13, 16, 17, 18, 16, 
-	13, 20, 21, 19, 23, 24, 22, 20, 
-	26, 25, 23, 28, 27, 27, 22, 29, 
-	13, 30, 13, 31, 31, 31, 13, 33, 
-	14, 14, 14, 32, 34, 14, 14, 14, 
-	32, 35, 35, 32, 36, 36, 36, 32, 
-	38, 14, 14, 14, 37, 15, 39, 14, 
-	14, 14, 37, 15, 40, 14, 14, 14, 
-	37, 15, 41, 14, 14, 14, 37, 15, 
-	42, 14, 14, 14, 37, 43, 14, 14, 
-	14, 37, 44, 44, 45, 45, 45, 45, 
-	46, 37, 47, 37, 48, 49, 1, 50, 
-	1, 51, 1, 52, 1, 7, 1, 53, 
-	1, 54, 1, 6, 1, 55, 1, 56, 
-	1, 7, 1, 57, 57, 1, 16, 17, 
-	18, 57, 8, 57, 16, 58, 29, 59, 
-	59, 1, 16, 17, 18, 57, 57, 16, 
-	1, 57, 60, 57, 29, 1, 57, 57, 
-	30, 1, 61, 61, 31, 31, 31, 1, 
-	62, 62, 36, 36, 36, 1, 63, 63, 
-	47, 1, 63, 63, 1, 0
-]
-
-class << self
-	attr_accessor :_simple_lexer_trans_targs
-	private :_simple_lexer_trans_targs, :_simple_lexer_trans_targs=
-end
-self._simple_lexer_trans_targs = [
-	2, 0, 3, 4, 32, 40, 5, 6, 
-	43, 0, 8, 20, 24, 0, 9, 44, 
-	10, 11, 13, 12, 45, 16, 12, 45, 
-	16, 14, 15, 14, 15, 46, 47, 48, 
-	0, 21, 22, 23, 49, 0, 25, 26, 
-	27, 28, 29, 30, 31, 51, 50, 50, 
-	33, 37, 34, 35, 36, 38, 39, 41, 
-	42, 7, 17, 19, 18, 7, 7, 7
-]
-
-class << self
-	attr_accessor :_simple_lexer_trans_actions
-	private :_simple_lexer_trans_actions, :_simple_lexer_trans_actions=
-end
-self._simple_lexer_trans_actions = [
-	0, 0, 0, 0, 0, 0, 0, 0, 
-	0, 26, 1, 1, 1, 15, 0, 7, 
-	0, 0, 0, 1, 17, 1, 0, 3, 
-	0, 1, 1, 0, 0, 0, 0, 0, 
-	20, 0, 5, 1, 0, 23, 0, 0, 
-	0, 0, 0, 5, 1, 1, 1, 0, 
-	0, 0, 0, 0, 0, 0, 0, 0, 
-	0, 0, 0, 1, 0, 9, 11, 13
-]
-
-class << self
-	attr_accessor :_simple_lexer_eof_actions
-	private :_simple_lexer_eof_actions, :_simple_lexer_eof_actions=
-end
-self._simple_lexer_eof_actions = [
-	0, 0, 0, 0, 0, 0, 0, 26, 
-	15, 15, 15, 15, 15, 15, 15, 15, 
-	15, 15, 15, 15, 20, 20, 20, 20, 
-	23, 23, 23, 23, 23, 23, 23, 23, 
-	0, 0, 0, 0, 0, 0, 0, 0, 
-	0, 0, 0, 0, 0, 0, 0, 0, 
-	9, 11, 13, 13
-]
-
-class << self
-	attr_accessor :simple_lexer_start
-end
-self.simple_lexer_start = 1;
-class << self
-	attr_accessor :simple_lexer_first_final
-end
-self.simple_lexer_first_final = 43;
-class << self
-	attr_accessor :simple_lexer_error
-end
-self.simple_lexer_error = 0;
-
-class << self
-	attr_accessor :simple_lexer_en_main
-end
-self.simple_lexer_en_main = 1;
-
-
-# line 61 "gen_vcfheaderline_parser.rl"
-# %% this just fixes our syntax highlighting...
-
-def self.run_lexer(buf, options = {})
-  do_debug = (options[:debug] == true)
-  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
-    puts "#{type}: #{data[ts...p].pack('c*')}" if do_debug
-    values << [type,data[ts...p].pack('c*')]
-  }
-
-  error_code = nil
-  
-  
-# line 242 "gen_vcfheaderline_parser.rb"
-begin
-	p ||= 0
-	pe ||= data.length
-	cs = simple_lexer_start
-end
-
-# line 80 "gen_vcfheaderline_parser.rl"
-  
-# line 251 "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
-	_trans = _simple_lexer_indicies[_trans]
-	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 23 "gen_vcfheaderline_parser.rl"
-		begin
- ts=p 		end
-when 1 then
-# line 24 "gen_vcfheaderline_parser.rl"
-		begin
-
-    emit.call(:value,data,ts,p)
-  		end
-when 2 then
-# line 28 "gen_vcfheaderline_parser.rl"
-		begin
-
-    emit.call(:kw,data,ts,p)
-  		end
-when 3 then
-# line 46 "gen_vcfheaderline_parser.rl"
-		begin
- emit.call(:key_word,data,ts,p) 		end
-when 4 then
-# line 47 "gen_vcfheaderline_parser.rl"
-		begin
- emit.call(:value,data,ts,p) 		end
-when 5 then
-# line 48 "gen_vcfheaderline_parser.rl"
-		begin
- emit.call(:value,data,ts,p) 		end
-when 6 then
-# line 50 "gen_vcfheaderline_parser.rl"
-		begin
- emit.call(:value,data,ts,p) 		end
-when 7 then
-# line 52 "gen_vcfheaderline_parser.rl"
-		begin
- error_code="ID"		end
-when 8 then
-# line 53 "gen_vcfheaderline_parser.rl"
-		begin
- error_code="Number"		end
-when 9 then
-# line 54 "gen_vcfheaderline_parser.rl"
-		begin
- error_code="key-value" 		end
-# line 376 "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 4 then
-# line 47 "gen_vcfheaderline_parser.rl"
-		begin
- emit.call(:value,data,ts,p) 		end
-when 5 then
-# line 48 "gen_vcfheaderline_parser.rl"
-		begin
- emit.call(:value,data,ts,p) 		end
-when 6 then
-# line 50 "gen_vcfheaderline_parser.rl"
-		begin
- emit.call(:value,data,ts,p) 		end
-when 7 then
-# line 52 "gen_vcfheaderline_parser.rl"
-		begin
- error_code="ID"		end
-when 8 then
-# line 53 "gen_vcfheaderline_parser.rl"
-		begin
- error_code="Number"		end
-when 9 then
-# line 54 "gen_vcfheaderline_parser.rl"
-		begin
- error_code="key-value" 		end
-# line 428 "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 81 "gen_vcfheaderline_parser.rl"
-
-  raise "ERROR: "+error_code+" in "+buf if error_code
-
-  begin
-    res = {}
-    # p values
-    values.each_slice(2) do | a,b |
-      # p '*',a,b
-      res[a[1]] = b[1]
-      # p h[:value] if h[:name]==:identifier or h[:name]==:value or h[:name]==:string
-    end
-  rescue
-    print "ERROR: "
-    p values
-    raise
-  end
-  p res if do_debug
-  res
-end
-    end
-  end 
-end
-
-if __FILE__ == $0
-
-lines = <<LINES
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth",Extra="Yes?">
-##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
-##INFO=<ID=PM,Number=0,Type=Flag,Description="Variant is Precious(Clinical,Pubmed Cited)">
-##INFO=<ID=VP,Number=1,Type=String,Description="Variation Property.  Documentation is at ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf",Source="dbsnp",Version="138">
-##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id.  The gene symbol and id are delimited by a colon (:), and each pair is delimited by a vertical bar (|)">
-##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Variant names from HGVS. The order of these variants corresponds to the order of the info in the other clinical  INFO tags.">
-##INFO=<ID=CLNHGVS1,Number=.,Type=String,Description="Variant names from \\"HGVS\\". The order of these 'variants' corresponds to the order of the info in the other clinical  INFO tags.">
-LINES
-
-lines.strip.split("\n").each { |s|
-  print s,"\n"
-  p BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(s, debug: false)
-}
-
-end # test