bin/snp-search in snp-search-0.23.0 vs bin/snp-search in snp-search-0.26.0

@@ -20,21 +20,29 @@
     puts help
   end
 end
 opts.parse
 
-  puts "You must supply the -n option, it's a required field" and exit unless opts[:name]
-  puts "You must supply the -r option, it's a required field" and exit unless opts[:reference_file]
-  puts "You must supply the -v option, it's a required field" and exit unless opts[:vcf_file] 
+  error_msg = ""
+
+  error_msg += "You must supply the -n option, it's a required field\n" unless opts[:name]
+  error_msg += "You must supply the -r option, it's a required field\n" unless opts[:reference_file]
+  error_msg += "You must supply the -v option, it's a required field" unless opts[:vcf_file]
+  
+  unless error_msg == "" 
+    puts error_msg
+    puts opts.help  unless opts.empty?
+    exit
+  end
    
   begin 
-  puts "#{opts[:reference_file]} file does not exist!" and exit unless File.exist?(opts[:reference_file])
+  abort "#{opts[:reference_file]} file does not exist!" unless File.exist?(opts[:reference_file])
   rescue
   end
   
   begin
-  puts "#{opts[:vcf_file]} file does not exist!" and exit unless File.exist?(opts[:vcf_file])
+  abort "#{opts[:vcf_file]} file does not exist!" unless File.exist?(opts[:vcf_file])
   rescue
   end
 
 begin
 # Enter the name of your database 
@@ -60,10 +68,10 @@
 
 # path for vcf file here
 vcf_mpileup_file = opts[:vcf_file]
 
 # The populate_features_and_annotations method populates the features and annotations.  It uses the embl/gbk file.
-populate_features_and_annotations(sequence_flatfile)
+# populate_features_and_annotations(sequence_flatfile)
 
 #The populate_snps_alleles_genotypes method populates the snps, alleles and genotypes.  It uses the vcf file, and if specified, the SNP quality cutoff and genotype quality cutoff
 populate_snps_alleles_genotypes(vcf_mpileup_file, opts[:cuttoff_snp].to_i, opts[:cuttoff_genotype].to_i)
 
 rescue