Merge pull request #15 from homonecloco/max_hits

Now the hit count is preserved

bin/polymarker.rb

@@ -392,7 +392,7 @@ def do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options)
 end
 
 kasp_container.add_primers_file(primer_3_output) if added_exons > 0
-header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,SNP_type,#{original_name},#{snp_in},common,primer_type,orientation,#{original_name}_TM,#{snp_in}_TM,common_TM,selected_from,product_size,errors,is_repetitive"
+header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,SNP_type,#{original_name},#{snp_in},common,primer_type,orientation,#{original_name}_TM,#{snp_in}_TM,common_TM,selected_from,product_size,errors,is_repetitive,hit_count"
 File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }
 
 File.open(output_to_order, "w") { |io|  io.write(kasp_container.print_primers_with_tails()) }

lib/bio/PolyploidTools/ExonContainer.rb

@@ -221,6 +221,7 @@ def remove_alignments_over_max_hits
         snp_array.each do |snp|
           if snp.exon_list.size > max_hits
             total_hits = snp.exon_list.size
+            snp.hit_count = total_hits
             snp.exon_list = {} 
             snp.repetitive = true
             snp.errors << "The marker is in a repetitive region (#{total_hits} hits to reference)"

lib/bio/PolyploidTools/SNP.rb

@@ -18,6 +18,7 @@ class SNP
     attr_accessor :max_hits
     attr_accessor :errors
     attr_accessor :repetitive
+    attr_accessor :hit_count
 
 
 
@@ -69,6 +70,7 @@ def initialize
       @exon_list = Hash.new {|hsh, key| hsh[key] = [] }
       @errors = Array.new
       @repetitive = false
+      @hit_count = 0
     end
 
     def to_polymarker_coordinates(flanking_size, total:nil)
@@ -340,8 +342,9 @@ def primer_3_all_strings(target_chromosome, parental)
         errors << "The sequence (#{seq_original.size}) is shorter than #{primer_3_min_seq_length}"
         return primer_3_propertes 
       end
-
-      if exon_list.size > max_hits
+      hit_count = exon_list.size
+      puts exon_list.inspect
+      if hit_count > max_hits
         errors << "The marker maps to #{exon_list.size} positions (max_hits: #{max_hits}). "
         repetitive = true
         return primer_3_propertes 

lib/bio/db/primer3.rb

@@ -60,6 +60,7 @@ class SNP
     attr_accessor :regions
     attr_accessor :primer3_errors
     attr_accessor :repetitive
+    attr_accessor :hit_count
 
     def line_1_name
       "#{gene}:#{position}#{original}>#{snp} #{line_1}}"
@@ -249,6 +250,7 @@ def values
     def print_primers
       to_print = values.dup
       to_print << @repetitive
+      to_print << hit_count
       to_print.join(",")
     end
 
@@ -765,7 +767,8 @@ def add_snp(snp_in)
       snp.position = snp_in.position
       snp.snp = snp_in.snp
       snp.repetitive = snp_in.repetitive
-
+      #puts snp_in.inspect
+      snp.hit_count = snp_in.hit_count
       snp.line_1 = @line_1
       snp.line_2 = @line_2 
       snp.snp_from = snp_in