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 CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA256:
3
- metadata.gz: e1dde0f369e105d6603efae5e1312d89233cf2e3601938093c57d2ebc408deeb
4
- data.tar.gz: f580aebdf6e6713c450008006dc5cfd371aff4ab443b6e9d12bc623661a22d54
3
+ metadata.gz: 80492a2607af467274ac7ca76979826e09dade8e59cba047a557c98448d71406
4
+ data.tar.gz: 94c59ed53e14840eb52ac2a628ba96a8bff6cc45f1490b66cb5bed8522eddafe
5
5
  SHA512:
6
- metadata.gz: 508347342dc0147269cc96a67a79f479d264ebd91d45d1b70d6fa7c484a4ea6a5cc7e481822bdf25910a8a2f9d5961e988b76f0244151c1052aa5a0333db8c22
7
- data.tar.gz: 060b9a465213d0447fa5e35e4b0ae9bc27cc3754e92615d6ac5b1214e902f11f95fbb002dd088e845efdb2c3bd9402b2f40ccad52d584dc6cbeac72fa97cf433
6
+ metadata.gz: f5e03604ce62a488b6053655f475583a2579e1c6b22effc0dbba069c6b469fc92294ec4c5674bf73644b8704f4441651652e45117bb6db7bbdb0ed6d5a8ff86e
7
+ data.tar.gz: 54ca702eb2348297f0a26d56f6fbb963da7dddf09a78a5783b9d4f6faac3b42e8213b814080852b2ce4f3c8dc61bad3233c2995660553d75ee77eb2f2e073290
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.9.1
1
+ 0.9.2
@@ -2,11 +2,11 @@
2
2
  # DO NOT EDIT THIS FILE DIRECTLY
3
3
  # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
4
4
  # -*- encoding: utf-8 -*-
5
- # stub: bio-polyploid-tools 0.9.1 ruby lib
5
+ # stub: bio-polyploid-tools 0.9.2 ruby lib
6
6
 
7
7
  Gem::Specification.new do |s|
8
8
  s.name = "bio-polyploid-tools".freeze
9
- s.version = "0.9.1"
9
+ s.version = "0.9.2"
10
10
 
11
11
  s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
12
12
  s.require_paths = ["lib".freeze]
@@ -219,9 +219,9 @@ module Bio::PolyploidTools
219
219
  def remove_alignments_over_max_hits
220
220
  @snp_map.each_pair do | gene, snp_array|
221
221
  snp_array.each do |snp|
222
- if snp.exon_list.size > max_hits
223
- total_hits = snp.exon_list.size
224
- snp.hit_count = total_hits
222
+ total_hits = snp.exon_list.size
223
+ snp.hit_count = total_hits
224
+ if total_hits > max_hits
225
225
  snp.exon_list = {}
226
226
  snp.repetitive = true
227
227
  snp.errors << "The marker is in a repetitive region (#{total_hits} hits to reference)"
@@ -68,6 +68,7 @@ module Bio::PolyploidTools
68
68
  @exon_list = Hash.new {|hsh, key| hsh[key] = [] }
69
69
  @errors = Array.new
70
70
  @repetitive = false
71
+ @hit_count = 0
71
72
  end
72
73
 
73
74
  def to_polymarker_coordinates(flanking_size, total:nil)
@@ -340,8 +341,8 @@ module Bio::PolyploidTools
340
341
  return primer_3_propertes
341
342
  end
342
343
 
343
- if @hit_count > @max_hits
344
- errors << "The marker maps to #{@hit_count} positions (max_hits: #{@max_hits}). "
344
+ if self.hit_count > self.max_hits
345
+ errors << "The marker maps to #{self.hit_count} positions (max_hits: #{self.max_hits}). "
345
346
  repetitive = true
346
347
  return primer_3_propertes
347
348
  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-polyploid-tools
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.9.1
4
+ version: 0.9.2
5
5
  platform: ruby
6
6
  authors:
7
7
  - Ricardo H. Ramirez-Gonzalez