gff3-fetch in bio-gff3-0.8.3

- old
+ new

@@ -14,13 +14,14 @@
 
   Where (NYI == Not Yet Implemented):
 
     --translate     : output as amino acid sequence 
     --validate      : validate GFF3 file by translating
+    --fix           : check 3-frame translation and fix, if possible 
+    --fix-wormbase  : fix 3-frame translation on ORFs named 'gene1'
     --no-assemble   : output each record as a sequence -- NYI
     --add-phase     : output records using phase (useful w. no-assemble CDS to AA) --NYI
-    --fix           : check 3-frame translation and fix, if possible -- NYI
   
   type is any valid type in the GFF3 definition. For example:
 
     mRNA            : assemble mRNA
     CDS             : assemble CDS 
@@ -140,10 +141,18 @@
   opts.on("--validate", "validate GFF3 file by translating") do |v|
     options.validate = v
     $stop_on_error = true  # replace global in near future
   end
 
+  opts.on("--fix", "Fix frame errors in the GFF3 definition") do |v|
+    options.fix = true
+  end
+
+  opts.on("--fix-wormbase", "Wormbase fix gene1 frame error") do |v|
+    options.fix_wormbase = true
+  end
+
   # opts.on("-q", "--quiet", "Run quietly") do |q|
   #   options.quiet = q
   # end
 
   # opts.on("-v", "--[no-]verbose", "Run verbosely") do |v|
@@ -172,9 +181,11 @@
   opts = {}
   opts[:validate] = options.validate
   opts[:cache_components] = options.cache
   opts[:cache_records]    = options.cache
   opts[:fasta_filename] = fastafn if fastafn
+  opts[:fix_wormbase] = options.fix_wormbase
+  opts[:fix] = options.fix
   gffdb = Bio::GFFbrowser::GFFdb.new(fn,opts)
   gff = gffdb.assembler
   writer = Bio::GFFbrowser::FastaWriter.new(options.translate, options.validate)
   case gfftype.downcase
     when 'mrna' 