bio-vcf 0.8.2 → 0.9.0

data/features/step_definitions/multisample.rb

@@ -37,6 +37,18 @@ Then(/^I expect rec\.info\.readposranksum to be (\d+)\.(\d+)$/) do |arg1, arg2|
   expect(@rec1.info.readposranksum).to eq 0.815
 end
 
+Then(/^I expect rec\.info\['dp'\] to be (\d+)$/) do |arg1|
+  expect(@rec1.info['dp']).to eq 1537
+end
+
+Then(/^I expect rec\.info\['ReadPosRankSum'\] to be (\d+)\.(\d+)$/) do |arg1, arg2|
+  expect(@rec1.info['ReadPosRankSum']).to eq 0.815
+end
+
+Then(/^I expect rec\.info\.fields to contain \["(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)"\]$/) do |arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, arg9, arg10, arg11, arg12, arg13, arg14, arg15|
+  expect(@rec1.info.fields).to eq ["AC", "AF", "AN", "BASEQRANKSUM", "DP", "DELS", "FS", "HAPLOTYPESCORE", "MLEAC", "MLEAF", "MQ", "MQ0", "MQRANKSUM", "QD", "READPOSRANKSUM"]
+end
+
 Then(/^I expect rec\.sample\.original\.gt to be "(.*?)"$/) do |arg1|
   expect(@rec1.sample['Original'].gt).to eq "0/1"
 end
@@ -161,3 +173,10 @@ Then(/^I expect r\.original\.gts\[(\d+)\] to be "(.*?)"$/) do |arg1, arg2|
   expect(@rec1.original.gts[arg1.to_i]).to eq arg2
 end
 
+Then(/^I expect r\.info\.end to be (\d+)$/) do |arg1|
+  expect(@rec1.info.end).to eq arg1.to_i
+end
+
+Then(/^I expect r\.info\.ciend to be (\d+)$/) do |arg1|
+  expect(@rec1.info.ciend).to eq arg1.to_i
+end

data/features/step_definitions/vcf_header.rb

@@ -43,6 +43,6 @@ Then(/^I expect vcf\.meta to contain all header meta information$/) do
   m = @vcf.meta
   expect(m['fileformat']).to eq "VCFv4.1"
   expect(m['FORMAT']['DP']['Number']).to eq "1"
-  expect(m.size).to be 6
+  expect(m.size).to be 9
 end
 

data/features/support/env.rb

@@ -1,12 +1,3 @@
-require 'bundler'
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
-
 # require 'mini/test'
 
 $LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')

data/lib/bio-vcf/pcows.rb

@@ -0,0 +1,210 @@
+# Parallel copy-on-write streaming (PCOWS)
+
+require 'tempfile'
+
+class PCOWS
+
+  RUNNINGEXT = 'part'
+  
+  def initialize(num_threads,name=File.basename(__FILE__),timeout=180)
+    num_threads = cpu_count() if not num_threads # FIXME: set to cpu_num by default
+    # $stderr.print "Using ",num_threads,"threads \n"
+    @num_threads = num_threads
+    @pid_list = []
+    @name = name
+    @timeout = timeout
+    if multi_threaded
+      @tmpdir =  Dir::mktmpdir(@name+'_')
+    end
+    @last_output = 0 # counter
+    @output_locked = nil
+  end
+
+  # Feed the worker func and state to COWS. Note that func is a lambda
+  # closure so it can pick up surrounding scope at invocation in
+  # addition to the data captured in 'state'.
+  
+  def submit_worker(func,state)
+    pid = nil
+    if multi_threaded
+      count = @pid_list.size+1
+      fn = mktmpfilename(count)
+      pid = fork do
+        # ---- This is running a new copy-on-write process
+        tempfn = fn+'.'+RUNNINGEXT
+        STDOUT.reopen(File.open(tempfn, 'w+'))
+        func.call(state).each { | line | print line }
+        STDOUT.flush
+        STDOUT.close
+        FileUtils::mv(tempfn,fn)
+        exit 0
+      end
+    else
+      # ---- Call in main process and output immediately
+      func.call(state).each { | line | print line }
+    end
+    @pid_list << [ pid,count,fn ]
+    return true
+  end
+
+  # Make sure no more than num_threads are running at the same time -
+  # this is achieved by checking the PID table and the running files
+  # in the tmpdir
+
+  def wait_for_worker_slot()
+    return if single_threaded
+    Timeout.timeout(@timeout) do
+    
+      while true
+        # ---- count running pids
+        running = @pid_list.reduce(0) do | sum, info |
+          (pid,count,fn) = info
+          if pid_or_file_running?(pid,fn)
+            sum+1
+          else
+            sum
+          end
+        end
+        return if running < @num_threads
+        $stderr.print "Waiting for slot (timeout=#{@timeout})\n"
+        sleep 0.1
+        
+      end
+    end
+  end
+
+  # ---- In this section the output gets collected and passed on to a
+  #      printer thread. This function makes sure the printing is
+  #      ordered and that no printers are running at the same
+  #      time. The printer thread should be doing as little processing
+  #      as possible.
+  #
+  #      In this implementation type==:by_line will call func for
+  #      each line. Otherwise it is called once with the filename.
+
+  def process_output(func=nil,type = :by_line, blocking=false)
+    return if single_threaded
+    output = lambda { |fn|
+      if type == :by_line
+        File.new(fn).each_line { |buf|
+          print buf
+        }
+      else
+        func.call(fn)
+      end
+      File.unlink(fn)
+    }
+    if @output_locked
+      (pid,count,fn) = @output_locked
+      return if File.exist?(fn)  # still processing
+      # on to the next one
+      @last_output += 1
+      @output_locked = nil
+    end
+    if info = @pid_list[@last_output]
+      (pid,count,fn) = info
+      $stderr.print "Processing #{fn}\n"
+      if File.exist?(fn)
+        # Yes! We have the next output, create outputter
+        if not blocking
+          pid = fork do
+            output.call(fn)
+            exit(0)
+          end
+          @output_locked = info
+        else
+          output.call(fn)
+        end
+      end
+    end
+  end
+
+  def wait_for_worker(info)
+    (pid,count,fn) = info
+    if pid_or_file_running?(pid,fn)
+      $stderr.print "Waiting up to #{@timeout} seconds for pid=#{pid} to complete\n"
+      begin
+        Timeout.timeout(@timeout) do
+          while not File.exist?(fn)  # wait for the result to appear
+            sleep 0.2
+          end
+        end
+        # Thread file should have gone:
+        raise "FATAL: child process appears to have crashed #{fn}" if not File.exist?(fn)
+        $stderr.print "OK pid=#{pid}, processing #{fn}\n"
+      rescue Timeout::Error
+        if pid_running?(pid)
+          # Kill it to speed up exit
+          Process.kill 9, pid
+          Process.wait pid
+        end
+        $stderr.print "FATAL: child process killed because it stopped responding, pid = #{pid}\n"
+      end
+    end
+  end
+  
+  # This is the final cleanup after the reader thread is done. All workers
+  # need to complete.
+  
+  def wait_for_workers()
+    return if single_threaded
+    @pid_list.each do |info|
+      wait_for_worker(info)
+    end
+  end
+
+  def process_remaining_output()
+    return if single_threaded
+    while @output_locked
+      sleep 0.2
+      process_output()
+    end
+    @pid_list.each do |info|
+      process_output(nil,:by_line,true)
+    end
+    # final cleanup
+    Dir.unlink(@tmpdir) if @tmpdir
+  end
+  
+  private
+  
+  def mktmpfilename(num,ext=nil)
+    @tmpdir+sprintf("/%0.6d-",num)+@name+(ext ? '.'+ext : '')
+  end
+  
+  def pid_or_file_running?(pid,fn)
+    (pid && pid_running?(pid)) or File.exist?(fn+'.'+RUNNINGEXT)
+  end
+  
+  def pid_running?(pid)
+    begin
+      fpid,status=Process.waitpid2(pid,Process::WNOHANG)
+    rescue Errno::ECHILD, Errno::ESRCH
+      return false
+    end
+    return true if nil == fpid && nil == status
+    return ! (status.exited? || status.signaled?)
+  end
+
+  def single_threaded
+    @num_threads == 1
+  end
+  
+  def multi_threaded
+    @num_threads > 1
+  end
+
+  def cpu_count
+    begin
+      return File.read('/proc/cpuinfo').scan(/^processor\s*:/).size if File.exist? '/proc/cpuinfo'
+      # Actually, the JVM does not allow fork...
+      return Java::Java.lang.Runtime.getRuntime.availableProcessors if defined? Java::Java
+    rescue LoadError
+      # Count on MAC
+      return Integer `sysctl -n hw.ncpu 2>/dev/null`
+    end
+    $stderr.print "Could not determine number of CPUs"
+    1
+  end
+
+end

data/lib/bio-vcf/vcfheader.rb

@@ -2,7 +2,7 @@
 # containing fields. Most fields are of 'key=value' type and appear
 # only once.  These can be retrieved with the find_field method.
 #
-# INFO and FORMAT fields are special as they appear multiple times
+# 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.
@@ -25,8 +25,8 @@ module BioVcf
       nil
     end
 
-    def VcfHeaderParser.parse_field(line)
-      BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(line, debug: false)
+    def VcfHeaderParser.parse_field(line, debug)
+      BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(line, debug: debug)
     end
   end
 
@@ -34,9 +34,11 @@ module BioVcf
 
     attr_reader :lines, :field
 
-    def initialize
+    def initialize(debug = false)
+      @debug = debug
       @lines = []
       @field = {}
+      @meta = nil
     end
 
     # Add a new field to the header
@@ -125,7 +127,7 @@ module BioVcf
         if value[0]
           str = value[0][0]
           # p str
-          v = VcfHeaderParser.parse_field(line)
+          v = VcfHeaderParser.parse_field(line,@debug)
           id = v['ID']
           res[id] = v
         end
@@ -138,25 +140,42 @@ module BioVcf
       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
-      res = { 'INFO' => {}, 'FORMAT' => {} }
+      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'
+          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['INFO'] = info()
+      res['FORMAT'] = format()
+      res['FILTER'] = filter()
+      res['contig'] = contig()
+      res['GATKCommandLine'] = gatkcommandline()
       # p [:res, res]
+      @meta = res # cache values
       res
     end
     

data/lib/bio-vcf/vcfheader_line.rb

@@ -2,38 +2,51 @@
 # 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.
+# 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 57 "gen_vcfheaderline_parser.rl"
+# line 75 "gen_vcfheaderline_parser.rl"
 
 =end
 
 
-# line 28 "gen_vcfheaderline_parser.rb"
+# 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, 4, 1, 5, 1, 6, 1, 
-	9, 2, 0, 1, 2, 7, 9, 2, 
-	8, 9, 3, 7, 8, 9
+	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
@@ -41,13 +54,23 @@ class << self
 	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
+	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
@@ -55,31 +78,94 @@ class << self
 	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
+	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
@@ -87,13 +173,23 @@ class << self
 	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
+	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
@@ -101,13 +197,23 @@ class << self
 	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, 
+	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, 5, 1, 1, 1, 
-	3, 3, 1, 0
+	0, 0, 0, 0, 0
 ]
 
 class << self
@@ -115,44 +221,23 @@ class << self
 	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
+	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
@@ -160,14 +245,88 @@ class << self
 	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
+	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
@@ -176,13 +335,87 @@ class << self
 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
+	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
@@ -190,13 +423,23 @@ class << self
 	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, 
+	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, 
-	9, 11, 13, 13
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0
 ]
 
 class << self
@@ -206,7 +449,7 @@ self.simple_lexer_start = 1;
 class << self
 	attr_accessor :simple_lexer_first_final
 end
-self.simple_lexer_first_final = 43;
+self.simple_lexer_first_final = 132;
 class << self
 	attr_accessor :simple_lexer_error
 end
@@ -218,11 +461,12 @@ end
 self.simple_lexer_en_main = 1;
 
 
-# line 61 "gen_vcfheaderline_parser.rl"
-# %% this just fixes our syntax highlighting...
+# 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 = []
@@ -231,23 +475,23 @@ def self.run_lexer(buf, options = {})
   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
+    $stderr.print "EMITTED: #{type}: #{data[ts...p].pack('c*')}\n" if do_debug
     values << [type,data[ts...p].pack('c*')]
   }
 
   error_code = nil
   
   
-# line 242 "gen_vcfheaderline_parser.rb"
+# line 486 "gen_vcfheaderline_parser.rb"
 begin
 	p ||= 0
 	pe ||= data.length
 	cs = simple_lexer_start
 end
 
-# line 80 "gen_vcfheaderline_parser.rl"
+# line 99 "gen_vcfheaderline_parser.rl"
   
-# line 251 "gen_vcfheaderline_parser.rb"
+# line 495 "gen_vcfheaderline_parser.rb"
 begin
 	_klen, _trans, _keys, _acts, _nacts = nil
 	_goto_level = 0
@@ -318,7 +562,6 @@ begin
 	     _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]
@@ -329,50 +572,78 @@ begin
 			_acts += 1
 			case _simple_lexer_actions[_acts - 1]
 when 0 then
-# line 23 "gen_vcfheaderline_parser.rl"
+# line 33 "gen_vcfheaderline_parser.rl"
 		begin
  ts=p 		end
 when 1 then
-# line 24 "gen_vcfheaderline_parser.rl"
+# line 34 "gen_vcfheaderline_parser.rl"
 		begin
 
     emit.call(:value,data,ts,p)
   		end
 when 2 then
-# line 28 "gen_vcfheaderline_parser.rl"
+# line 38 "gen_vcfheaderline_parser.rl"
 		begin
 
     emit.call(:kw,data,ts,p)
   		end
 when 3 then
-# line 46 "gen_vcfheaderline_parser.rl"
+# line 58 "gen_vcfheaderline_parser.rl"
 		begin
  emit.call(:key_word,data,ts,p) 		end
 when 4 then
-# line 47 "gen_vcfheaderline_parser.rl"
+# line 59 "gen_vcfheaderline_parser.rl"
 		begin
  emit.call(:value,data,ts,p) 		end
 when 5 then
-# line 48 "gen_vcfheaderline_parser.rl"
+# line 60 "gen_vcfheaderline_parser.rl"
 		begin
  emit.call(:value,data,ts,p) 		end
 when 6 then
-# line 50 "gen_vcfheaderline_parser.rl"
+# line 62 "gen_vcfheaderline_parser.rl"
 		begin
  emit.call(:value,data,ts,p) 		end
 when 7 then
-# line 52 "gen_vcfheaderline_parser.rl"
+# line 65 "gen_vcfheaderline_parser.rl"
 		begin
- error_code="ID"		end
+ emit.call(:value,data,ts,p) 		end
 when 8 then
-# line 53 "gen_vcfheaderline_parser.rl"
+# line 67 "gen_vcfheaderline_parser.rl"
 		begin
- error_code="Number"		end
+ debug("ID FOUND") 		end
 when 9 then
-# line 54 "gen_vcfheaderline_parser.rl"
+# 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="key-value" 		end
-# line 376 "gen_vcfheaderline_parser.rb"
+ 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
@@ -400,31 +671,31 @@ when 9 then
 		__nacts -= 1
 		__acts += 1
 		case _simple_lexer_actions[__acts - 1]
-when 4 then
-# line 47 "gen_vcfheaderline_parser.rl"
+when 9 then
+# line 67 "gen_vcfheaderline_parser.rl"
 		begin
- emit.call(:value,data,ts,p) 		end
-when 5 then
-# line 48 "gen_vcfheaderline_parser.rl"
+ error_code="Malformed ID"		end
+when 10 then
+# line 68 "gen_vcfheaderline_parser.rl"
 		begin
- emit.call(:value,data,ts,p) 		end
-when 6 then
-# line 50 "gen_vcfheaderline_parser.rl"
+ error_code="Version"		end
+when 11 then
+# line 69 "gen_vcfheaderline_parser.rl"
 		begin
- emit.call(:value,data,ts,p) 		end
-when 7 then
-# line 52 "gen_vcfheaderline_parser.rl"
+ error_code="Number"		end
+when 13 then
+# line 70 "gen_vcfheaderline_parser.rl"
 		begin
- error_code="ID"		end
-when 8 then
-# line 53 "gen_vcfheaderline_parser.rl"
+ error_code="Date"		end
+when 14 then
+# line 71 "gen_vcfheaderline_parser.rl"
 		begin
- error_code="Number"		end
-when 9 then
-# line 54 "gen_vcfheaderline_parser.rl"
+ error_code="GATK"		end
+when 16 then
+# line 72 "gen_vcfheaderline_parser.rl"
 		begin
- error_code="key-value" 		end
-# line 428 "gen_vcfheaderline_parser.rb"
+ error_code="unknown key-value " 		end
+# line 699 "gen_vcfheaderline_parser.rb"
 		end # eof action switch
 	end
 	if _trigger_goto
@@ -438,7 +709,7 @@ end
 	end
 	end
 
-# line 81 "gen_vcfheaderline_parser.rl"
+# line 100 "gen_vcfheaderline_parser.rl"
 
   raise "ERROR: "+error_code+" in "+buf if error_code
 
@@ -446,8 +717,11 @@ end
     res = {}
     # p values
     values.each_slice(2) do | a,b |
-      # p '*',a,b
-      res[a[1]] = b[1]
+      $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
@@ -455,7 +729,7 @@ end
     p values
     raise
   end
-  p res if do_debug
+  $stderr.print(res,"\n") if do_debug
   res
 end
     end
@@ -464,7 +738,19 @@ 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">
@@ -473,11 +759,20 @@ lines = <<LINES
 ##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"
-  p BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(s, debug: false)
+  # 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