bio-polyploid-tools 0.9.4 → 0.9.5
Sign up to get free protection for your applications and to get access to all the features.
- 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
|