bio-polyploid-tools 0.8.8 → 0.8.9

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 54a35758a75bfdda5b273263a9ea83b59e22f0e6
+SHA256:
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+  data.tar.gz: 5f597fa54fc9d9be8a10efb27ecbacf261d4285a950a24c2b49b8f6ad09f954a
 SHA512:
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data/VERSION

@@ -1 +1 @@
-0.8.8
+0.8.9

data/bio-polyploid-tools.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.8.8 ruby lib
+# stub: bio-polyploid-tools 0.8.9 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.8.8"
+  s.version = "0.8.9"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Ricardo H.  Ramirez-Gonzalez".freeze]
-  s.date = "2018-08-10"
+  s.date = "2018-08-16"
   s.description = "Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat".freeze
   s.email = "ricardo.ramirez-gonzalez@jic.ac.uk".freeze
   s.executables = ["bfr.rb".freeze, "blast_triads.rb".freeze, "blast_triads_promoters.rb".freeze, "count_variations.rb".freeze, "filter_blat_by_target_coverage.rb".freeze, "filter_exonerate_by_identity.rb".freeze, "find_best_blat_hit.rb".freeze, "find_best_exonerate.rb".freeze, "find_homoeologue_variations.rb".freeze, "get_longest_hsp_blastx_triads.rb".freeze, "hexaploid_primers.rb".freeze, "homokaryot_primers.rb".freeze, "mafft_triads.rb".freeze, "mafft_triads_promoters.rb".freeze, "map_markers_to_contigs.rb".freeze, "markers_in_region.rb".freeze, "mask_triads.rb".freeze, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "tag_stats.rb".freeze, "vcfLineToTable.rb".freeze]
@@ -113,7 +113,7 @@ Gem::Specification.new do |s|
     "test/data/BS00068396_51_contigs.nin",
     "test/data/BS00068396_51_contigs.nsq",
     "test/data/BS00068396_51_exonerate.tab",
-    "test/data/BS00068396_51_for_polymarker.fa",
+    "test/data/BS00068396_51_for_polymarker.txt",
     "test/data/BS00068396_51_genes.txt",
     "test/data/IWGSC_CSS_1AL_scaff_1455974.fa",
     "test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa",
@@ -180,7 +180,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "2.6.14".freeze
+  s.rubygems_version = "2.7.4".freeze
   s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze
 
   if s.respond_to? :specification_version then

data/lib/bio/PolyploidTools/SNP.rb

@@ -342,10 +342,9 @@ 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
-      puts exon_list.inspect
-      if hit_count > max_hits
-        errors << "The marker maps to #{exon_list.size} positions (max_hits: #{max_hits}). "
+      @hit_count = exon_list.size
+      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

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.8.8
+  version: 0.8.9
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-10 00:00:00.000000000 Z
+date: 2018-08-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -233,7 +233,7 @@ files:
 - test/data/BS00068396_51_contigs.nin
 - test/data/BS00068396_51_contigs.nsq
 - test/data/BS00068396_51_exonerate.tab
-- test/data/BS00068396_51_for_polymarker.fa
+- test/data/BS00068396_51_for_polymarker.txt
 - test/data/BS00068396_51_genes.txt
 - test/data/IWGSC_CSS_1AL_scaff_1455974.fa
 - test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa
@@ -317,7 +317,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.14
+rubygems_version: 2.7.4
 signing_key: 
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology