vcfToPolyMarker.rb in bio-polyploid-tools-0.10.0

- old
+ new

@@ -14,11 +14,11 @@
 options = {}
 options[:arm_selection] = Bio::PolyploidTools::ChromosomeArm.getArmSelection("nrgene");
 
 
 OptionParser.new do |opts|
-	opts.banner = "Usage: polymarker.rb [options]"
+	opts.banner = "Usage: vcfToPolyMarker.rb [options]"
 
 	opts.on("-c", "--reference FILE", "File with genome reference to use as database") do |o|
 		options[:path_to_contigs] = o
 	end
 
@@ -73,10 +73,10 @@
 		#puts header
 		next
 	end
 	line.chomp!
 	#puts line
-	snp = Bio::PolyploidTools::SNP.parseVCF( line , options[:arm_selection])
+	snp = Bio::PolyploidTools::SNP.parseVCF( line , chr_arm_parser: options[:arm_selection])
 	#puts snp.inspect
 	snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size: 100)
 	puts [snp.gene, snp.chromosome ,snp.to_polymarker_sequence(100)].join(",")
 end
\ No newline at end of file