bio-polyploid-tools 0.9.1 → 0.9.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/bio-polyploid-tools.gemspec +2 -2
- data/lib/bio/PolyploidTools/ExonContainer.rb +3 -3
- data/lib/bio/PolyploidTools/SNP.rb +3 -2
- metadata +1 -1
checksums.yaml
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@@ -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: 80492a2607af467274ac7ca76979826e09dade8e59cba047a557c98448d71406
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data.tar.gz: 94c59ed53e14840eb52ac2a628ba96a8bff6cc45f1490b66cb5bed8522eddafe
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: f5e03604ce62a488b6053655f475583a2579e1c6b22effc0dbba069c6b469fc92294ec4c5674bf73644b8704f4441651652e45117bb6db7bbdb0ed6d5a8ff86e
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data.tar.gz: 54ca702eb2348297f0a26d56f6fbb963da7dddf09a78a5783b9d4f6faac3b42e8213b814080852b2ce4f3c8dc61bad3233c2995660553d75ee77eb2f2e073290
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data/VERSION
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@@ -1 +1 @@
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1
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0.9.
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0.9.2
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data/bio-polyploid-tools.gemspec
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@@ -2,11 +2,11 @@
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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 0.9.2 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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s.version = "0.9.2"
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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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@@ -219,9 +219,9 @@ module Bio::PolyploidTools
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def remove_alignments_over_max_hits
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@snp_map.each_pair do | gene, snp_array|
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snp_array.each do |snp|
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total_hits = snp.exon_list.size
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snp.hit_count = total_hits
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if total_hits > max_hits
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snp.exon_list = {}
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snp.repetitive = true
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snp.errors << "The marker is in a repetitive region (#{total_hits} hits to reference)"
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@@ -68,6 +68,7 @@ module Bio::PolyploidTools
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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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@hit_count = 0
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end
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def to_polymarker_coordinates(flanking_size, total:nil)
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@@ -340,8 +341,8 @@ module Bio::PolyploidTools
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return primer_3_propertes
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end
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if
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errors << "The marker maps to #{
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if self.hit_count > self.max_hits
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errors << "The marker maps to #{self.hit_count} positions (max_hits: #{self.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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