bio-vcf 0.8.0 → 0.9.4

data/lib/bio-vcf/vcfheader.rb

@@ -1,3 +1,14 @@
+# This module parses the VCF header. A header consists of lines
+# containing fields. Most fields are of 'key=value' type and appear
+# only once.  These can be retrieved with the find_field method.
+#
+# INFO, FORMAT and contig fields are special as they appear multiple times
+# and contain multiple key values (identified by an ID field).
+# To retrieve these call 'info' and 'format' functions respectively,
+# which return a hash on the contained ID.
+#
+# For the INFO and FORMAT fields a Ragel parser is used, mostly to
+# deal with embedded quoted fields.
 
 module BioVcf
 
@@ -13,21 +24,30 @@ module BioVcf
       end
       nil
     end
+
+    def VcfHeaderParser.parse_field(line, debug)
+      BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(line, debug: debug)
+    end
   end
 
   class VcfHeader
 
-    attr_reader :lines
+    attr_reader :lines, :field
 
-    def initialize
+    def initialize(debug = false)
+      @debug = debug
       @lines = []
+      @field = {}
+      @meta = nil
+      @cached_filter_index = {}
     end
 
+    # Add a new field to the header
     def add line
-      @lines << line.strip
+      @lines += line.split(/\n/)
     end
 
-    # Add a key value list to the header
+    # Push a special key value list to the header
     def tag h
       h2 = h.dup
       [:show_help,:skip_header,:verbose,:quiet,:debug].each { |key| h2.delete(key) }
@@ -60,13 +80,21 @@ module BioVcf
     end
 
     def samples
-      @samples ||= column_names[9..-1]
+      @samples ||= if column_names.size > 8
+                     column_names[9..-1]
+                   else
+                     []
+                   end
     end
 
     def samples_index_array
       @all_samples_index ||= column_names[9..-1].fill{|i| i}
     end
 
+    def num_samples
+      @num_samples ||= ( samples == nil ? 0 : samples.size )
+    end
+
     def sample_index
       return @sample_index if @sample_index
       index = {}
@@ -74,6 +102,118 @@ module BioVcf
       @sample_index = index
       index
     end
-  end
 
+    # Give a list of samples (by index and/or name) and return 0-based index values
+    # The cache has to be able to hanle multiple lists - that is why it is a hash.
+    def sample_subset_index list
+      cached = @cached_filter_index[list]
+      if cached
+        l = cached
+      else
+        l = []
+        list = samples_index_array() if not list
+        list.each { |i|
+          value = 
+            begin 
+              Integer(i)
+            rescue
+              idx = samples.index(i)
+              if idx != nil
+                idx
+              else
+                raise "Unknown sample name '#{i}'"
+              end
+            end
+          l << value
+        }
+        @cached_filter_index[list] = l
+      end
+      l
+    end
+    
+    # Look for a line in the header with the field name and return the
+    # value, otherwise return nil
+    def find_field name
+      return field[name] if field[name]
+      @lines.each do | line |
+        value = line.scan(/###{name}=(.*)/)
+        if value[0]
+          v = value[0][0]
+          field[name] = v
+          return v
+        end
+      end
+      nil
+    end
+
+    # Look for all the lines that match the field name and return
+    # a hash of hashes. An empty hash is returned when there are
+    # no matches.
+    def find_fields name
+      res = {}
+      @lines.each do | line |
+        value = line.scan(/###{name}=<(.*)>/)
+        if value[0]
+          str = value[0][0]
+          # p str
+          v = VcfHeaderParser.parse_field(line,@debug)
+          id = v['ID']
+          res[id] = v
+        end
+      end
+      # p res
+      res
+    end
+
+    def format 
+      find_fields('FORMAT')
+    end
+
+    def filter
+      find_fields('FILTER')
+    end
+
+    def contig
+      find_fields('contig')
+    end
+
+    def info
+      find_fields('INFO')
+    end
+
+    def gatkcommandline
+      find_fields('GATKCommandLine')
+    end
+    
+    def meta
+      return @meta if @meta
+      res = { 'INFO' => {}, 'FORMAT' => {}, 'FILTER' => {}, 'contig' => {}, 'GATKCommandLine' => {} }
+      @lines.each do | line |
+        value = line.scan(/##(.*?)=(.*)/)
+        if value[0]
+          k,v = value[0]
+          if k != 'FORMAT' and k != 'INFO' and k != 'FILTER' and k != 'contig' and k != 'GATKCommandLine'
+            # p [k,v]
+            res[k] = v
+          end
+        end
+      end
+      res['INFO'] = info()
+      res['FORMAT'] = format()
+      res['FILTER'] = filter()
+      res['contig'] = contig()
+      res['GATKCommandLine'] = gatkcommandline()
+      # p [:res, res]
+      @meta = res # cache values
+      res
+    end
+    
+    def method_missing(m, *args, &block)
+      name = m.to_s
+      value = find_field(name)
+      return value if value
+      raise "Unknown VCF header query '#{name}'"
+    end
+
+  end
 end

data/lib/bio-vcf/vcfheader_line.rb

@@ -0,0 +1,778 @@
+
+# line 1 "gen_vcfheaderline_parser.rl"
+# Ragel lexer for VCF-header
+#
+# This is compact a parser/lexer for the VCF header format. Bio-vcf
+# uses the parser to generate meta information that can be output to
+# (for example) JSON format. The advantage of using ragel as a 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 ragel parser/lexer generates valid Ruby; it should be
+# fairly trivial to generate python/C/JAVA instead. Note that this
+# edition validates ID and Number fields only.  Other fields are
+# dumped 'AS IS'.
+#
+# Note the .rb version is generated from ./ragel/gen_vcfheaderline_parser.rl
+#
+# by Pjotr Prins (c) 2014/2015
+
+module BioVcf
+
+  module VcfHeaderParser
+
+    module RagelKeyValues
+
+      def self.debug msg
+        # nothing
+	# $stderr.print "DEBUG: ",msg,"\n"
+      end
+      
+=begin
+
+# line 75 "gen_vcfheaderline_parser.rl"
+
+=end
+
+
+# line 38 "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, 15, 1, 16, 2, 0, 1, 
+	2, 4, 15, 2, 6, 15, 2, 7, 
+	15, 2, 9, 16, 2, 10, 16, 2, 
+	11, 16, 2, 12, 15, 2, 13, 16, 
+	2, 14, 16, 3, 5, 8, 15, 6, 
+	9, 10, 13, 11, 14, 16
+]
+
+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, 7, 8, 9, 10, 
+	13, 26, 35, 49, 51, 53, 58, 60, 
+	62, 62, 62, 64, 70, 72, 77, 80, 
+	91, 101, 111, 121, 131, 141, 151, 161, 
+	171, 181, 191, 201, 211, 221, 231, 241, 
+	251, 261, 270, 275, 277, 279, 279, 281, 
+	283, 283, 293, 303, 313, 322, 327, 329, 
+	331, 331, 333, 335, 335, 345, 354, 360, 
+	371, 381, 391, 401, 411, 421, 430, 438, 
+	440, 445, 448, 458, 468, 478, 488, 498, 
+	508, 517, 524, 526, 528, 533, 535, 537, 
+	537, 537, 549, 559, 569, 579, 589, 599, 
+	609, 619, 629, 639, 649, 659, 669, 671, 
+	672, 673, 674, 675, 676, 677, 678, 679, 
+	680, 681, 682, 683, 684, 685, 686, 687, 
+	688, 689, 690, 691, 692, 693, 694, 695, 
+	696, 697, 698, 699, 700
+]
+
+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, 71, 73, 99, 76, 
+	84, 61, 44, 60, 62, 67, 68, 73, 
+	78, 86, 97, 108, 48, 57, 65, 90, 
+	98, 122, 46, 61, 95, 48, 57, 65, 
+	90, 97, 122, 34, 39, 44, 46, 60, 
+	62, 43, 45, 48, 57, 65, 90, 97, 
+	122, 34, 92, 34, 92, 34, 39, 44, 
+	60, 62, 39, 92, 39, 92, 48, 57, 
+	44, 46, 60, 62, 48, 57, 48, 57, 
+	44, 60, 62, 48, 57, 44, 60, 62, 
+	44, 46, 60, 62, 95, 48, 57, 65, 
+	90, 97, 122, 46, 61, 95, 111, 48, 
+	57, 65, 90, 97, 122, 46, 61, 95, 
+	109, 48, 57, 65, 90, 97, 122, 46, 
+	61, 95, 109, 48, 57, 65, 90, 97, 
+	122, 46, 61, 95, 97, 48, 57, 65, 
+	90, 98, 122, 46, 61, 95, 110, 48, 
+	57, 65, 90, 97, 122, 46, 61, 95, 
+	100, 48, 57, 65, 90, 97, 122, 46, 
+	61, 76, 95, 48, 57, 65, 90, 97, 
+	122, 46, 61, 95, 105, 48, 57, 65, 
+	90, 97, 122, 46, 61, 95, 110, 48, 
+	57, 65, 90, 97, 122, 46, 61, 95, 
+	101, 48, 57, 65, 90, 97, 122, 46, 
+	61, 79, 95, 48, 57, 65, 90, 97, 
+	122, 46, 61, 95, 112, 48, 57, 65, 
+	90, 97, 122, 46, 61, 95, 116, 48, 
+	57, 65, 90, 97, 122, 46, 61, 95, 
+	105, 48, 57, 65, 90, 97, 122, 46, 
+	61, 95, 111, 48, 57, 65, 90, 97, 
+	122, 46, 61, 95, 110, 48, 57, 65, 
+	90, 97, 122, 46, 61, 95, 115, 48, 
+	57, 65, 90, 97, 122, 46, 61, 95, 
+	48, 57, 65, 90, 97, 122, 34, 39, 
+	44, 60, 62, 34, 92, 34, 92, 39, 
+	92, 39, 92, 46, 61, 95, 97, 48, 
+	57, 65, 90, 98, 122, 46, 61, 95, 
+	116, 48, 57, 65, 90, 97, 122, 46, 
+	61, 95, 101, 48, 57, 65, 90, 97, 
+	122, 46, 61, 95, 48, 57, 65, 90, 
+	97, 122, 34, 39, 44, 60, 62, 34, 
+	92, 34, 92, 39, 92, 39, 92, 46, 
+	61, 68, 95, 48, 57, 65, 90, 97, 
+	122, 46, 61, 95, 48, 57, 65, 90, 
+	97, 122, 48, 57, 65, 90, 97, 122, 
+	44, 46, 60, 62, 95, 48, 57, 65, 
+	90, 97, 122, 46, 61, 95, 117, 48, 
+	57, 65, 90, 97, 122, 46, 61, 95, 
+	109, 48, 57, 65, 90, 97, 122, 46, 
+	61, 95, 98, 48, 57, 65, 90, 97, 
+	122, 46, 61, 95, 101, 48, 57, 65, 
+	90, 97, 122, 46, 61, 95, 114, 48, 
+	57, 65, 90, 97, 122, 46, 61, 95, 
+	48, 57, 65, 90, 97, 122, 43, 45, 
+	46, 65, 71, 82, 48, 57, 48, 57, 
+	44, 60, 62, 48, 57, 44, 60, 62, 
+	46, 61, 95, 101, 48, 57, 65, 90, 
+	97, 122, 46, 61, 95, 114, 48, 57, 
+	65, 90, 97, 122, 46, 61, 95, 115, 
+	48, 57, 65, 90, 97, 122, 46, 61, 
+	95, 105, 48, 57, 65, 90, 97, 122, 
+	46, 61, 95, 111, 48, 57, 65, 90, 
+	97, 122, 46, 61, 95, 110, 48, 57, 
+	65, 90, 97, 122, 46, 61, 95, 48, 
+	57, 65, 90, 97, 122, 34, 39, 44, 
+	60, 62, 48, 57, 34, 92, 34, 92, 
+	34, 39, 44, 60, 62, 39, 92, 39, 
+	92, 44, 60, 62, 95, 45, 46, 48, 
+	57, 65, 90, 97, 122, 46, 61, 95, 
+	115, 48, 57, 65, 90, 97, 122, 46, 
+	61, 95, 115, 48, 57, 65, 90, 97, 
+	122, 46, 61, 95, 101, 48, 57, 65, 
+	90, 97, 122, 46, 61, 95, 109, 48, 
+	57, 65, 90, 97, 122, 46, 61, 95, 
+	98, 48, 57, 65, 90, 97, 122, 46, 
+	61, 95, 108, 48, 57, 65, 90, 97, 
+	122, 46, 61, 95, 121, 48, 57, 65, 
+	90, 97, 122, 46, 61, 95, 101, 48, 
+	57, 65, 90, 97, 122, 46, 61, 95, 
+	110, 48, 57, 65, 90, 97, 122, 46, 
+	61, 95, 103, 48, 57, 65, 90, 97, 
+	122, 46, 61, 95, 116, 48, 57, 65, 
+	90, 97, 122, 46, 61, 95, 104, 48, 
+	57, 65, 90, 97, 122, 73, 79, 76, 
+	84, 69, 82, 82, 77, 65, 65, 84, 
+	75, 67, 111, 109, 109, 97, 110, 100, 
+	76, 105, 110, 101, 78, 70, 79, 111, 
+	110, 116, 105, 103, 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, 5, 1, 1, 1, 3, 
+	7, 3, 6, 2, 2, 5, 2, 2, 
+	0, 0, 0, 4, 0, 3, 3, 5, 
+	4, 4, 4, 4, 4, 4, 4, 4, 
+	4, 4, 4, 4, 4, 4, 4, 4, 
+	4, 3, 5, 2, 2, 0, 2, 2, 
+	0, 4, 4, 4, 3, 5, 2, 2, 
+	0, 2, 2, 0, 4, 3, 0, 5, 
+	4, 4, 4, 4, 4, 3, 6, 0, 
+	3, 3, 4, 4, 4, 4, 4, 4, 
+	3, 5, 2, 2, 5, 2, 2, 0, 
+	0, 4, 4, 4, 4, 4, 4, 4, 
+	4, 4, 4, 4, 4, 4, 2, 1, 
+	1, 1, 1, 1, 1, 1, 1, 1, 
+	1, 1, 1, 1, 1, 1, 1, 1, 
+	1, 1, 1, 1, 1, 1, 1, 1, 
+	1, 1, 1, 1, 0
+]
+
+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, 0, 
+	3, 3, 4, 0, 0, 0, 0, 0, 
+	0, 0, 1, 1, 1, 1, 0, 3, 
+	3, 3, 3, 3, 3, 3, 3, 3, 
+	3, 3, 3, 3, 3, 3, 3, 3, 
+	3, 3, 0, 0, 0, 0, 0, 0, 
+	0, 3, 3, 3, 3, 0, 0, 0, 
+	0, 0, 0, 0, 3, 3, 3, 3, 
+	3, 3, 3, 3, 3, 3, 1, 1, 
+	1, 0, 3, 3, 3, 3, 3, 3, 
+	3, 1, 0, 0, 0, 0, 0, 0, 
+	0, 4, 3, 3, 3, 3, 3, 3, 
+	3, 3, 3, 3, 3, 3, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 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, 10, 12, 14, 16, 
+	20, 31, 38, 49, 52, 55, 61, 64, 
+	67, 68, 69, 71, 77, 79, 84, 88, 
+	97, 105, 113, 121, 129, 137, 145, 153, 
+	161, 169, 177, 185, 193, 201, 209, 217, 
+	225, 233, 240, 246, 249, 252, 253, 256, 
+	259, 260, 268, 276, 284, 291, 297, 300, 
+	303, 304, 307, 310, 311, 319, 326, 330, 
+	339, 347, 355, 363, 371, 379, 386, 394, 
+	396, 401, 405, 413, 421, 429, 437, 445, 
+	453, 460, 467, 470, 473, 479, 482, 485, 
+	486, 487, 496, 504, 512, 520, 528, 536, 
+	544, 552, 560, 568, 576, 584, 592, 595, 
+	597, 599, 601, 603, 605, 607, 609, 611, 
+	613, 615, 617, 619, 621, 623, 625, 627, 
+	629, 631, 633, 635, 637, 639, 641, 643, 
+	645, 647, 649, 651, 653
+]
+
+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, 0, 4, 102, 110, 124, 
+	127, 0, 5, 0, 6, 0, 7, 0, 
+	8, 8, 132, 0, 24, 49, 60, 64, 
+	74, 90, 97, 9, 9, 9, 0, 9, 
+	10, 9, 9, 9, 9, 0, 11, 14, 
+	8, 22, 8, 132, 18, 23, 23, 23, 
+	0, 13, 17, 12, 13, 17, 12, 11, 
+	14, 8, 8, 132, 0, 13, 16, 15, 
+	13, 16, 15, 15, 12, 19, 0, 8, 
+	20, 8, 132, 19, 0, 21, 0, 8, 
+	8, 132, 21, 0, 8, 8, 132, 0, 
+	8, 23, 8, 132, 23, 23, 23, 23, 
+	0, 9, 10, 9, 25, 9, 9, 9, 
+	0, 9, 10, 9, 26, 9, 9, 9, 
+	0, 9, 10, 9, 27, 9, 9, 9, 
+	0, 9, 10, 9, 28, 9, 9, 9, 
+	0, 9, 10, 9, 29, 9, 9, 9, 
+	0, 9, 10, 9, 30, 9, 9, 9, 
+	0, 9, 10, 31, 9, 9, 9, 9, 
+	0, 9, 10, 9, 32, 9, 9, 9, 
+	0, 9, 10, 9, 33, 9, 9, 9, 
+	0, 9, 10, 9, 34, 9, 9, 9, 
+	0, 9, 10, 35, 9, 9, 9, 9, 
+	0, 9, 10, 9, 36, 9, 9, 9, 
+	0, 9, 10, 9, 37, 9, 9, 9, 
+	0, 9, 10, 9, 38, 9, 9, 9, 
+	0, 9, 10, 9, 39, 9, 9, 9, 
+	0, 9, 10, 9, 40, 9, 9, 9, 
+	0, 9, 10, 9, 41, 9, 9, 9, 
+	0, 9, 42, 9, 9, 9, 9, 0, 
+	43, 46, 8, 8, 132, 0, 42, 45, 
+	44, 42, 45, 44, 44, 42, 48, 47, 
+	42, 48, 47, 47, 9, 10, 9, 50, 
+	9, 9, 9, 0, 9, 10, 9, 51, 
+	9, 9, 9, 0, 9, 10, 9, 52, 
+	9, 9, 9, 0, 9, 53, 9, 9, 
+	9, 9, 0, 54, 57, 8, 8, 132, 
+	0, 53, 56, 55, 53, 56, 55, 55, 
+	53, 59, 58, 53, 59, 58, 58, 9, 
+	10, 61, 9, 9, 9, 9, 0, 9, 
+	62, 9, 9, 9, 9, 0, 63, 63, 
+	63, 0, 8, 63, 8, 132, 63, 63, 
+	63, 63, 0, 9, 10, 9, 65, 9, 
+	9, 9, 0, 9, 10, 9, 66, 9, 
+	9, 9, 0, 9, 10, 9, 67, 9, 
+	9, 9, 0, 9, 10, 9, 68, 9, 
+	9, 9, 0, 9, 10, 9, 69, 9, 
+	9, 9, 0, 9, 70, 9, 9, 9, 
+	9, 0, 71, 71, 73, 73, 73, 73, 
+	72, 0, 72, 0, 8, 8, 132, 72, 
+	0, 8, 8, 132, 0, 9, 10, 9, 
+	75, 9, 9, 9, 0, 9, 10, 9, 
+	76, 9, 9, 9, 0, 9, 10, 9, 
+	77, 9, 9, 9, 0, 9, 10, 9, 
+	78, 9, 9, 9, 0, 9, 10, 9, 
+	79, 9, 9, 9, 0, 9, 10, 9, 
+	80, 9, 9, 9, 0, 9, 81, 9, 
+	9, 9, 9, 0, 82, 85, 8, 8, 
+	132, 89, 0, 84, 88, 83, 84, 88, 
+	83, 82, 85, 8, 8, 132, 0, 84, 
+	87, 86, 84, 87, 86, 86, 83, 8, 
+	8, 132, 89, 89, 89, 89, 89, 0, 
+	9, 10, 9, 91, 9, 9, 9, 0, 
+	9, 10, 9, 92, 9, 9, 9, 0, 
+	9, 10, 9, 93, 9, 9, 9, 0, 
+	9, 10, 9, 94, 9, 9, 9, 0, 
+	9, 10, 9, 95, 9, 9, 9, 0, 
+	9, 10, 9, 96, 9, 9, 9, 0, 
+	9, 10, 9, 61, 9, 9, 9, 0, 
+	9, 10, 9, 98, 9, 9, 9, 0, 
+	9, 10, 9, 99, 9, 9, 9, 0, 
+	9, 10, 9, 100, 9, 9, 9, 0, 
+	9, 10, 9, 101, 9, 9, 9, 0, 
+	9, 10, 9, 69, 9, 9, 9, 0, 
+	103, 107, 0, 104, 0, 105, 0, 106, 
+	0, 6, 0, 108, 0, 109, 0, 5, 
+	0, 111, 0, 112, 0, 113, 0, 114, 
+	0, 115, 0, 116, 0, 117, 0, 118, 
+	0, 119, 0, 120, 0, 121, 0, 122, 
+	0, 123, 0, 6, 0, 125, 0, 126, 
+	0, 6, 0, 128, 0, 129, 0, 130, 
+	0, 131, 0, 6, 0, 0, 0
+]
+
+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, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 1, 1, 1, 1, 
+	1, 1, 1, 1, 1, 1, 47, 0, 
+	7, 0, 0, 0, 0, 11, 0, 0, 
+	9, 0, 9, 9, 0, 1, 1, 1, 
+	0, 13, 1, 1, 3, 0, 0, 0, 
+	0, 9, 9, 9, 0, 13, 1, 1, 
+	3, 0, 0, 0, 0, 0, 11, 9, 
+	0, 9, 9, 0, 0, 0, 11, 9, 
+	9, 9, 0, 0, 9, 9, 9, 0, 
+	16, 0, 16, 16, 0, 0, 0, 0, 
+	0, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 7, 0, 0, 0, 0, 0, 
+	40, 0, 5, 0, 0, 0, 0, 40, 
+	0, 0, 9, 9, 9, 0, 13, 1, 
+	1, 3, 0, 0, 0, 13, 1, 1, 
+	3, 0, 0, 0, 0, 7, 0, 0, 
+	0, 0, 0, 37, 0, 7, 0, 0, 
+	0, 0, 0, 37, 0, 7, 0, 0, 
+	0, 0, 0, 37, 0, 5, 0, 0, 
+	0, 0, 37, 0, 0, 34, 34, 34, 
+	0, 13, 1, 1, 3, 0, 0, 0, 
+	13, 1, 1, 3, 0, 0, 0, 0, 
+	7, 0, 0, 0, 0, 0, 25, 0, 
+	5, 0, 0, 0, 0, 25, 1, 1, 
+	1, 25, 43, 0, 43, 43, 0, 0, 
+	0, 0, 0, 0, 7, 0, 0, 0, 
+	0, 0, 31, 0, 7, 0, 0, 0, 
+	0, 0, 31, 0, 7, 0, 0, 0, 
+	0, 0, 31, 0, 7, 0, 0, 0, 
+	0, 0, 31, 0, 7, 0, 0, 0, 
+	0, 0, 31, 0, 5, 0, 0, 0, 
+	0, 31, 1, 1, 1, 1, 1, 1, 
+	1, 31, 0, 31, 22, 22, 22, 0, 
+	0, 22, 22, 22, 0, 0, 7, 0, 
+	0, 0, 0, 0, 28, 0, 7, 0, 
+	0, 0, 0, 0, 28, 0, 7, 0, 
+	0, 0, 0, 0, 28, 0, 7, 0, 
+	0, 0, 0, 0, 28, 0, 7, 0, 
+	0, 0, 0, 0, 28, 0, 7, 0, 
+	0, 0, 0, 0, 28, 0, 5, 0, 
+	0, 0, 0, 28, 0, 0, 9, 9, 
+	9, 1, 0, 13, 1, 1, 3, 0, 
+	0, 0, 0, 9, 9, 9, 0, 13, 
+	1, 1, 3, 0, 0, 0, 0, 19, 
+	19, 19, 0, 0, 0, 0, 0, 0, 
+	0, 7, 0, 0, 0, 0, 0, 25, 
+	0, 7, 0, 0, 0, 0, 0, 25, 
+	0, 7, 0, 0, 0, 0, 0, 25, 
+	0, 7, 0, 0, 0, 0, 0, 25, 
+	0, 7, 0, 0, 0, 0, 0, 25, 
+	0, 7, 0, 0, 0, 0, 0, 25, 
+	0, 7, 0, 0, 0, 0, 0, 25, 
+	0, 7, 0, 0, 0, 0, 0, 31, 
+	0, 7, 0, 0, 0, 0, 0, 31, 
+	0, 7, 0, 0, 0, 0, 0, 31, 
+	0, 7, 0, 0, 0, 0, 0, 31, 
+	0, 7, 0, 0, 0, 0, 0, 31, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0
+]
+
+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, 0, 
+	47, 11, 0, 11, 11, 0, 11, 11, 
+	11, 11, 11, 0, 11, 0, 0, 0, 
+	40, 40, 40, 40, 40, 40, 40, 40, 
+	40, 40, 40, 40, 40, 40, 40, 40, 
+	40, 40, 0, 40, 40, 40, 40, 40, 
+	40, 37, 37, 37, 37, 0, 37, 37, 
+	37, 37, 37, 37, 25, 25, 25, 0, 
+	31, 31, 31, 31, 31, 31, 31, 31, 
+	0, 0, 28, 28, 28, 28, 28, 28, 
+	28, 0, 28, 28, 0, 28, 28, 28, 
+	28, 0, 25, 25, 25, 25, 25, 25, 
+	25, 31, 31, 31, 31, 31, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0
+]
+
+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 = 132;
+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 79 "gen_vcfheaderline_parser.rl"
+# %% this just fixes syntax highlighting...
+
+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
+    end
+  end 
+end
+
+if __FILE__ == $0
+
+gatkcommandline = <<LINE1
+##GATKCommandLine=<ID=CombineVariants,Version=3.2-2-gec30cee,Date="Thu Oct 30 13:41:59 CET 2014",Epoch=1414672919266,CommandLineOptions="analysis_type=CombineVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/hpc/cog_bioinf/GENOMES/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=/hpc/cog_bioinf/data/robert/testIAP/testSubsetExome/tmp/testSubsetExome.filtered_snps.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=/hpc/cog_bioinf/data/robert/testIAP/testSubsetExome/tmp/testSubsetExome.filtered_indels.vcf)])] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub genotypemergeoption=UNSORTED filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=null printComplexMerges=false filteredAreUncalled=false minimalVCF=false excludeNonVariants=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+LINE1
+
+h = {}
+s = gatkcommandline.strip
+# print s,"\n"
+result = BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(s, debug: true)
+# h[result['ID']] = result
+# p result
+
+lines = <<LINES
+##FILTER=<ID=HaplotypeScoreHigh,Description="HaplotypeScore > 13.0">
+##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.">
+##contig=<ID=XXXY12>
+##contig=<ID=Y,length=59373566>
+LINES
+
+h = {}
+lines.strip.split("\n").each { |s|
+  # print s,"\n"
+  result = BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(s, debug: true)
+  h[result['ID']] = result
+  p result
+}
+p h
+
+raise "ERROR" if h != {"HaplotypeScoreHigh"=>{"ID"=>"HaplotypeScoreHigh", "Description"=>"HaplotypeScore > 13.0"}, "GT"=>{"ID"=>"GT", "Number"=>"1", "Type"=>"String", "Description"=>"Genotype"}, "DP"=>{"ID"=>"DP", "Number"=>"1", "Type"=>"Integer", "Description"=>"Total read depth", "Extra"=>"Yes?"}, "DP4"=>{"ID"=>"DP4", "Number"=>"4", "Type"=>"Integer", "Description"=>"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"}, "PM"=>{"ID"=>"PM", "Number"=>"0", "Type"=>"Flag", "Description"=>"Variant is Precious(Clinical,Pubmed Cited)"}, "VP"=>{"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"}, "GENEINFO"=>{"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 (|)"}, "CLNHGVS"=>{"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."}, "CLNHGVS1"=>{"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."}, "XXXY12"=>{"ID"=>"XXXY12"}, "Y"=>{"ID"=>"Y", "length"=>59373566}}
+
+
+end # test