bio-polyploid-tools 0.8.9 → 0.9.0
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- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/bin/polymarker.rb +1 -1
- data/bio-polyploid-tools.gemspec +2 -2
- data/lib/bio/PolyploidTools/SNP.rb +4 -7
- 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: fcdf390e75bab0dee7b1c3032f17030a1a307a04937a96a1401c34e2583feac2
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4
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data.tar.gz: 3ef3ebeeb7290f6cb4da7fa1f19d5faa868ee2d4cb79def3bddff863c796b5eb
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: cebf0a197414ba8633f5d5dcd1c3cdb17c6ea7ec7868658544fd8cdc4e42da6460e022de68e431d8ec3a44bf1505a881ae56817bff3c9d50b5ef4202e386ca7d
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7
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data.tar.gz: 53fafe20fe479eadfa89a880fbfd36c1a447736c3909b40d7bc519d4fc7360bef8a4c49c1a9029d1360754b04336e1ca736131eb62e390cd079036f6ea0a3bad
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.
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1
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+
0.9.0
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data/bin/polymarker.rb
CHANGED
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.
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# stub: bio-polyploid-tools 0.9.0 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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9
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-
s.version = "0.
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9
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+
s.version = "0.9.0"
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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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@@ -20,8 +20,6 @@ module Bio::PolyploidTools
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attr_accessor :repetitive
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attr_accessor :hit_count
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-
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#Format:
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#Gene_name,Original,SNP_Pos,pos,chromosome
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#A_comp0_c0_seq1,C,519,A,2A
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@@ -70,7 +68,6 @@ module Bio::PolyploidTools
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70
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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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@@ -129,7 +126,6 @@ module Bio::PolyploidTools
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else
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exon_list[arm] << exon
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end
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-
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end
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def covered_region
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@@ -333,6 +329,7 @@ module Bio::PolyploidTools
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def primer_3_all_strings(target_chromosome, parental)
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+
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pr = primer_region(target_chromosome, parental )
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primer_3_propertes = Array.new
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@@ -342,9 +339,9 @@ module Bio::PolyploidTools
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errors << "The sequence (#{seq_original.size}) is shorter than #{primer_3_min_seq_length}"
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return primer_3_propertes
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end
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-
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-
if
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-
errors << "The marker maps to #{
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+
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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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