bio-polyploid-tools 0.9.0 → 0.9.1

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: f580aebdf6e6713c450008006dc5cfd371aff4ab443b6e9d12bc623661a22d54
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data/VERSION

@@ -1 +1 @@
-0.9.0
+0.9.1

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 0.9.0 ruby lib
+# stub: bio-polyploid-tools 0.9.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.9.0"
+  s.version = "0.9.1"
 
   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 = "2018-08-16"
+  s.date = "2018-08-17"
   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]

data/lib/bio/PolyploidTools/SNP.rb

@@ -64,7 +64,7 @@ module Bio::PolyploidTools
       @primer_3_min_seq_length = 50
       @variation_free_region = 0
       @contig = false
-      @max_hits = 10
+      @max_hits = 8
       @exon_list = Hash.new {|hsh, key| hsh[key] = [] }
       @errors = Array.new
       @repetitive = false
@@ -340,8 +340,8 @@ 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 @hit_count > @max_hits
+        errors << "The marker maps to #{@hit_count} positions (max_hits: #{@max_hits}). "
         repetitive = true
         return primer_3_propertes 
       end

data/lib/bio/db/primer3.rb

@@ -250,7 +250,7 @@ module Bio::DB::Primer3
     def print_primers
       to_print = values.dup
       to_print << @repetitive
-      to_print << hit_count
+      to_print << @hit_count
       to_print.join(",")
     end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.9.0
+  version: 0.9.1
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-16 00:00:00.000000000 Z
+date: 2018-08-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio