bio-polyploid-tools 0.9.0 → 0.9.1
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- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/bio-polyploid-tools.gemspec +3 -3
- data/lib/bio/PolyploidTools/SNP.rb +3 -3
- data/lib/bio/db/primer3.rb +1 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: e1dde0f369e105d6603efae5e1312d89233cf2e3601938093c57d2ebc408deeb
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4
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data.tar.gz: f580aebdf6e6713c450008006dc5cfd371aff4ab443b6e9d12bc623661a22d54
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 508347342dc0147269cc96a67a79f479d264ebd91d45d1b70d6fa7c484a4ea6a5cc7e481822bdf25910a8a2f9d5961e988b76f0244151c1052aa5a0333db8c22
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7
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data.tar.gz: 060b9a465213d0447fa5e35e4b0ae9bc27cc3754e92615d6ac5b1214e902f11f95fbb002dd088e845efdb2c3bd9402b2f40ccad52d584dc6cbeac72fa97cf433
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.9.
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1
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+
0.9.1
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data/bio-polyploid-tools.gemspec
CHANGED
@@ -2,16 +2,16 @@
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2
2
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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-
# stub: bio-polyploid-tools 0.9.
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+
# stub: bio-polyploid-tools 0.9.1 ruby lib
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Gem::Specification.new do |s|
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s.name = "bio-polyploid-tools".freeze
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-
s.version = "0.9.
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9
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+
s.version = "0.9.1"
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10
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s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
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s.require_paths = ["lib".freeze]
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s.authors = ["Ricardo H. Ramirez-Gonzalez".freeze]
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-
s.date = "2018-08-
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+
s.date = "2018-08-17"
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s.description = "Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat".freeze
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s.email = "ricardo.ramirez-gonzalez@jic.ac.uk".freeze
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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]
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@@ -64,7 +64,7 @@ module Bio::PolyploidTools
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@primer_3_min_seq_length = 50
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@variation_free_region = 0
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@contig = false
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-
@max_hits =
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+
@max_hits = 8
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@exon_list = Hash.new {|hsh, key| hsh[key] = [] }
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@errors = Array.new
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@repetitive = false
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@@ -340,8 +340,8 @@ module Bio::PolyploidTools
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return primer_3_propertes
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end
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-
if hit_count > max_hits
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-
errors << "The marker maps to #{hit_count} positions (max_hits: #{max_hits}). "
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+
if @hit_count > @max_hits
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+
errors << "The marker maps to #{@hit_count} positions (max_hits: #{@max_hits}). "
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repetitive = true
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return primer_3_propertes
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end
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data/lib/bio/db/primer3.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
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1
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--- !ruby/object:Gem::Specification
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name: bio-polyploid-tools
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version: !ruby/object:Gem::Version
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-
version: 0.9.
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+
version: 0.9.1
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platform: ruby
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authors:
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- Ricardo H. Ramirez-Gonzalez
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2018-08-
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+
date: 2018-08-17 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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