bio-polyploid-tools 0.9.1 → 0.9.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/VERSION

@@ -1 +1 @@
-0.9.1
+0.9.2

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 0.9.1 ruby lib
+# stub: bio-polyploid-tools 0.9.2 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.9.1"
+  s.version = "0.9.2"
 
   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/ExonContainer.rb

@@ -219,9 +219,9 @@ module Bio::PolyploidTools
     def remove_alignments_over_max_hits
       @snp_map.each_pair do | gene, snp_array| 
         snp_array.each do |snp|
-          if snp.exon_list.size > max_hits
-            total_hits = snp.exon_list.size
-            snp.hit_count = total_hits
+          total_hits = snp.exon_list.size
+          snp.hit_count = total_hits
+          if total_hits > max_hits
             snp.exon_list = {} 
             snp.repetitive = true
             snp.errors << "The marker is in a repetitive region (#{total_hits} hits to reference)"

data/lib/bio/PolyploidTools/SNP.rb

@@ -68,6 +68,7 @@ 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)
@@ -340,8 +341,8 @@ module Bio::PolyploidTools
         return primer_3_propertes 
       end
       
-      if @hit_count > @max_hits
-        errors << "The marker maps to #{@hit_count} positions (max_hits: #{@max_hits}). "
+      if self.hit_count > self.max_hits
+        errors << "The marker maps to #{self.hit_count} positions (max_hits: #{self.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: 0.9.1
+  version: 0.9.2
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez