bio-polyploid-tools 0.9.1 → 0.9.2
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- 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
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: 80492a2607af467274ac7ca76979826e09dade8e59cba047a557c98448d71406
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4
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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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7
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data.tar.gz: 54ca702eb2348297f0a26d56f6fbb963da7dddf09a78a5783b9d4f6faac3b42e8213b814080852b2ce4f3c8dc61bad3233c2995660553d75ee77eb2f2e073290
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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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+
0.9.2
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data/bio-polyploid-tools.gemspec
CHANGED
@@ -2,11 +2,11 @@
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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 0.9.2 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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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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-
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-
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-
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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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