bio-polyploid-tools 1.1.1 → 1.1.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/SECURITY.md

@@ -0,0 +1,16 @@
+# Security Policy
+
+## Supported Versions
+
+The following table shows the currently supported version. 
+
+| Version | Supported          |
+| ------- | ------------------ |
+| 1.1.x   | :white_check_mark: |
+| 1.0.x   | :x:                |
+| 0.x.x   | :x:                |
+
+
+## Reporting a Vulnerability
+
+If you find a vulneravility, please submit a comment in the security tab

data/VERSION

@@ -1 +1 @@
-1.1.1
+1.1.2

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 1.1.1 ruby lib
+# stub: bio-polyploid-tools 1.1.2 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "1.1.1"
+  s.version = "1.1.2"
 
   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 = "2019-11-03"
+  s.date = "2020-03-18"
   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, "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, "marker_to_vcf.rb".freeze, "markers_in_region.rb".freeze, "mask_triads.rb".freeze, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "polymarker_deletions.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "tag_stats.rb".freeze, "vcfLineToTable.rb".freeze, "vcfToPolyMarker.rb".freeze]
@@ -23,6 +23,7 @@ Gem::Specification.new do |s|
     "Gemfile",
     "README.md",
     "Rakefile",
+    "SECURITY.md",
     "VERSION",
     "bin/bfr.rb",
     "bin/blast_triads.rb",
@@ -183,7 +184,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "2.7.7".freeze
+  s.rubygems_version = "3.0.8".freeze
   s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze
 
   if s.respond_to? :specification_version then

data/lib/bio/BIOExtensions.rb

@@ -64,7 +64,7 @@ end
 
 class Bio::NucleicAcid
 
-  IUPAC_CODES = {
+  IUPAC_CODES ||= {
 
     'y' => 'ct',
     'r' => 'ag',

data/lib/bio/PolyploidTools/NoSNPSequence.rb

@@ -222,7 +222,7 @@ module Bio::PolyploidTools
         end
     end
 
-    def primer_3_all_strings(target_chromosome, parental) 
+    def primer_3_all_strings(target_chromosome, parental, max_specific_primers: nil) 
       #puts "primer_3_all_strings: #{target_chromosome} #{parental}"
       pr = primer_region(target_chromosome, parental )
       #puts pr.inspect

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 1.1.1
+  version: 1.1.2
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-11-03 00:00:00.000000000 Z
+date: 2020-03-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -145,6 +145,7 @@ files:
 - Gemfile
 - README.md
 - Rakefile
+- SECURITY.md
 - VERSION
 - bin/bfr.rb
 - bin/blast_triads.rb
@@ -321,8 +322,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.7
+rubygems_version: 3.0.8
 signing_key: 
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology