bio-polyploid-tools 0.9.4 → 0.9.5
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 +5 -5
- data/VERSION +1 -1
- data/bio-polyploid-tools.gemspec +4 -4
- data/lib/bio/PolyploidTools/ExonContainer.rb +1 -1
- metadata +3 -3
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
|
-
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
2
|
+
SHA256:
|
|
3
|
+
metadata.gz: 8430ec0c051e44642cabc28c9208f620cf6703f05c56b172c1cb924e06da6cbd
|
|
4
|
+
data.tar.gz: 104e83c6297886d6ab29a59691abf89708756dec7047b343193098f4438faa1f
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: f9635645ace5fda87f37522e30f3aae3081d67f162ee030f0de400049be2e4a1b8d061afd8da402278db5032451a524f84dbd48c222beafef945f4ad79e3c77b
|
|
7
|
+
data.tar.gz: 4bef3618f54865796f973fff7fdfc80ccb8ffaec826d78d000368308c2b1e540d1704d052718fe060d226c0ba0d4f57c2301c3b854d9c8ae3fa2f2f5a4719f41
|
data/VERSION
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
0.9.
|
|
1
|
+
0.9.5
|
data/bio-polyploid-tools.gemspec
CHANGED
|
@@ -2,16 +2,16 @@
|
|
|
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.
|
|
5
|
+
# stub: bio-polyploid-tools 0.9.5 ruby lib
|
|
6
6
|
|
|
7
7
|
Gem::Specification.new do |s|
|
|
8
8
|
s.name = "bio-polyploid-tools".freeze
|
|
9
|
-
s.version = "0.9.
|
|
9
|
+
s.version = "0.9.5"
|
|
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]
|
|
13
13
|
s.authors = ["Ricardo H. Ramirez-Gonzalez".freeze]
|
|
14
|
-
s.date = "2018-08-
|
|
14
|
+
s.date = "2018-08-20"
|
|
15
15
|
s.description = "Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat".freeze
|
|
16
16
|
s.email = "ricardo.ramirez-gonzalez@jic.ac.uk".freeze
|
|
17
17
|
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]
|
|
@@ -181,7 +181,7 @@ Gem::Specification.new do |s|
|
|
|
181
181
|
]
|
|
182
182
|
s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
|
|
183
183
|
s.licenses = ["MIT".freeze]
|
|
184
|
-
s.rubygems_version = "2.
|
|
184
|
+
s.rubygems_version = "2.7.4".freeze
|
|
185
185
|
s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze
|
|
186
186
|
|
|
187
187
|
if s.respond_to? :specification_version then
|
|
@@ -218,7 +218,7 @@ module Bio::PolyploidTools
|
|
|
218
218
|
def remove_alignments_over_max_hits
|
|
219
219
|
@snp_map.each_pair do | gene, snp_array|
|
|
220
220
|
snp_array.each do |snp|
|
|
221
|
-
total_hits = snp.exon_list.map {
|
|
221
|
+
total_hits = snp.exon_list.map {|e| e[1].size}.reduce(0,:+)
|
|
222
222
|
snp.hit_count = total_hits
|
|
223
223
|
if total_hits > max_hits
|
|
224
224
|
snp.exon_list = {}
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: bio-polyploid-tools
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.9.
|
|
4
|
+
version: 0.9.5
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Ricardo H. Ramirez-Gonzalez
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2018-08-
|
|
11
|
+
date: 2018-08-20 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: bio
|
|
@@ -318,7 +318,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
318
318
|
version: '0'
|
|
319
319
|
requirements: []
|
|
320
320
|
rubyforge_project:
|
|
321
|
-
rubygems_version: 2.
|
|
321
|
+
rubygems_version: 2.7.4
|
|
322
322
|
signing_key:
|
|
323
323
|
specification_version: 4
|
|
324
324
|
summary: Tool to work with polyploids, NGS and molecular biology
|