ExonContainer.rb in bio-polyploid-tools-1.0.0

- old
+ new

@@ -74,11 +74,10 @@
       path = opts[:alig_path]
       chromosomes[name] = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
     end
     
     def add_snp(snp)
-      #TODO: add to the snp the maximum number of hits? 
       snp.max_hits = self.max_hits
       @snp_map[snp.gene] = Array.new unless   @snp_map[snp.gene] 
       @snp_map[snp.gene] << snp
 
     end
@@ -139,10 +138,11 @@
           #puts snp.inspect
 
           begin 
             file.puts snp.aligned_sequences_fasta
           rescue Exception=>e
+            #puts snp.inspect
             @missing_exons << snp.to_s
             $stderr.puts "print_fasta_snp_exones:" + snp.to_s + ":" + e.to_s
             $stderr.puts "Local position: #{snp.local_position}"
             $stderr.puts "Local position: #{snp.parental_sequences.to_s}"
             $stderr.puts e.backtrace
@@ -158,11 +158,11 @@
         snp_array.each do |snp|
           string = ""
           begin 
             primer_3_min_seq_length
             string = snp.primer_3_string( snp.chromosome, parental )
-            #TODO: add tan error to the SNP this snp has more than max_hits. Or maybe inside the SNP file. 
-            #puts "print_primer_3_exons: #{string.size}"
+            #TODO: add tan error to the SNP this snp has more than max_hits. 
+            #Or maybe inside the SNP file. 
             if string.size > 0
               file.puts string
               added += 1
             end 
            rescue Exception=>e
\ No newline at end of file