snp-search 2.10.2 → 2.10.7
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.
- data/VERSION +1 -1
- data/lib/output_information_methods.rb +2 -2
- data/snp-search.gemspec +1 -1
- metadata +2 -2
data/VERSION
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
2.10.
|
|
1
|
+
2.10.7
|
|
@@ -19,7 +19,7 @@ def output_information_methods(snps, outfile, cuttoff_genotype, cuttoff_snp, inf
|
|
|
19
19
|
snp.alleles.each do |allele|
|
|
20
20
|
next if snp.alleles.any?{|allele| allele.base.length > 1} # indel
|
|
21
21
|
if allele.id != snp.reference_allele_id
|
|
22
|
-
|
|
22
|
+
|
|
23
23
|
# get annotation (if there is any) for each SNP
|
|
24
24
|
features = Feature.joins(:snps).where("snps.id = ?", snp.id)
|
|
25
25
|
|
|
@@ -37,7 +37,7 @@ def output_information_methods(snps, outfile, cuttoff_genotype, cuttoff_snp, inf
|
|
|
37
37
|
ref_base = Bio::Sequence.auto(Allele.find(snp.reference_allele_id).base)
|
|
38
38
|
snp_base = Bio::Sequence.auto(allele.base)
|
|
39
39
|
# count snps now: after you have selected the snps with gqs and snp_qual greater than the threshold.
|
|
40
|
-
|
|
40
|
+
snps_counter += 1
|
|
41
41
|
# If the feature is empty then just output basic information about the snp.
|
|
42
42
|
|
|
43
43
|
if features.empty?
|
data/snp-search.gemspec
CHANGED
|
@@ -5,7 +5,7 @@
|
|
|
5
5
|
|
|
6
6
|
Gem::Specification.new do |s|
|
|
7
7
|
s.name = "snp-search"
|
|
8
|
-
s.version = "2.10.
|
|
8
|
+
s.version = "2.10.7"
|
|
9
9
|
|
|
10
10
|
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
|
11
11
|
s.authors = ["Ali Al-Shahib", "Anthony Underwood"]
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: snp-search
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 2.10.
|
|
4
|
+
version: 2.10.7
|
|
5
5
|
prerelease:
|
|
6
6
|
platform: ruby
|
|
7
7
|
authors:
|
|
@@ -227,7 +227,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
|
227
227
|
version: '0'
|
|
228
228
|
segments:
|
|
229
229
|
- 0
|
|
230
|
-
hash:
|
|
230
|
+
hash: 323554498078972222
|
|
231
231
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
232
232
|
none: false
|
|
233
233
|
requirements:
|