bio-polyploid-tools 0.8.9 → 0.9.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  data.tar.gz: 3ef3ebeeb7290f6cb4da7fa1f19d5faa868ee2d4cb79def3bddff863c796b5eb
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+  data.tar.gz: 53fafe20fe479eadfa89a880fbfd36c1a447736c3909b40d7bc519d4fc7360bef8a4c49c1a9029d1360754b04336e1ca736131eb62e390cd079036f6ea0a3bad

data/VERSION

@@ -1 +1 @@
-0.8.9
+0.9.0

data/bin/polymarker.rb

@@ -39,7 +39,7 @@ options[:min_identity] = 90
 options[:scoring] = :genome_specific
 options[:database]  = false
 options[:filter_best]  = false
-options[:max_hits] = 10
+options[:max_hits] = 8
 options[:aligner] = :exonerate
 
 

data/bio-polyploid-tools.gemspec

@@ -2,11 +2,11 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.8.9 ruby lib
+# stub: bio-polyploid-tools 0.9.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.8.9"
+  s.version = "0.9.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]

data/lib/bio/PolyploidTools/SNP.rb

@@ -20,8 +20,6 @@ module Bio::PolyploidTools
     attr_accessor :repetitive
     attr_accessor :hit_count
 
-
-
     #Format: 
     #Gene_name,Original,SNP_Pos,pos,chromosome
     #A_comp0_c0_seq1,C,519,A,2A
@@ -70,7 +68,6 @@ module Bio::PolyploidTools
       @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)
@@ -129,7 +126,6 @@ module Bio::PolyploidTools
       else
          exon_list[arm] << exon 
       end
-        
     end
 
     def covered_region
@@ -333,6 +329,7 @@ module Bio::PolyploidTools
 
 
     def primer_3_all_strings(target_chromosome, parental) 
+
       pr = primer_region(target_chromosome, parental )
       primer_3_propertes = Array.new
 
@@ -342,9 +339,9 @@ module Bio::PolyploidTools
         errors << "The sequence (#{seq_original.size}) is shorter than #{primer_3_min_seq_length}"
         return primer_3_propertes 
       end
-      @hit_count = exon_list.size
-      if @hit_count > max_hits
-        errors << "The marker maps to #{@hit_count} positions (max_hits: #{max_hits}). "
+      
+      if hit_count > max_hits
+        errors << "The marker maps to #{hit_count} positions (max_hits: #{max_hits}). "
         repetitive = true
         return primer_3_propertes 
       end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.8.9
+  version: 0.9.0
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez