snp-search 0.33.0 → 0.34.0

data/VERSION

@@ -1 +1 @@
-0.33.0
+0.34.0

data/lib/snp-search.rb

@@ -83,17 +83,20 @@ puts "Adding SNPs........"
 				    ref_base = details[3]
 				    snp_base = details[4]
 				    snp_qual = details [5]
+				    format = details[8].split(":")
+				    gt = format.index("GT")
+				    gq = format.index("GQ")
 				    samples = details[9..-1]
 			     	
 			     	next if ref_base.size != 1 || snp_base.size != 1 # exclude indels
 				    genotypes = samples.map do |s| 
-				      pl, gt, gq = s.chomp.split(":")
-				      gt
+				      format_values = s.chomp.split(":")
+				      format_values[gt]
 				    end
 
 				    genotypes_qualities = samples.map do |s| 
-				      pl, gt, gq = s.chomp.split(":")
-				      gq
+				      format_values = s.chomp.split(":")
+				      format_values[gq]
 				    end
 
 				    high_quality_variant_genotypes = Array.new # this will be filled with the indicies of genotypes that are "1/1" and have a quality >= 30

data/snp-search.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "snp-search"
-  s.version = "0.33.0"
+  s.version = "0.34.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ali Al-Shahib", "Anthony Underwood"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: snp-search
 version: !ruby/object:Gem::Version
-  version: 0.33.0
+  version: 0.34.0
   prerelease: 
 platform: ruby
 authors:
@@ -14,7 +14,7 @@ date: 2012-01-11 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2158704900 !ruby/object:Gem::Requirement
+  requirement: &2166762620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: 3.1.3
   type: :runtime
   prerelease: false
-  version_requirements: *2158704900
+  version_requirements: *2166762620
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2158704300 !ruby/object:Gem::Requirement
+  requirement: &2166762140 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -33,10 +33,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2158704300
+  version_requirements: *2166762140
 - !ruby/object:Gem::Dependency
   name: slop
-  requirement: &2158703720 !ruby/object:Gem::Requirement
+  requirement: &2166761620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -44,10 +44,10 @@ dependencies:
         version: 2.4.0
   type: :runtime
   prerelease: false
-  version_requirements: *2158703720
+  version_requirements: *2166761620
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2158703220 !ruby/object:Gem::Requirement
+  requirement: &2166761060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +55,10 @@ dependencies:
         version: 1.3.4
   type: :runtime
   prerelease: false
-  version_requirements: *2158703220
+  version_requirements: *2166761060
 - !ruby/object:Gem::Dependency
   name: activerecord-import
-  requirement: &2158702700 !ruby/object:Gem::Requirement
+  requirement: &2166760580 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 0.2.8
   type: :runtime
   prerelease: false
-  version_requirements: *2158702700
+  version_requirements: *2166760580
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2158702100 !ruby/object:Gem::Requirement
+  requirement: &2166760100 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2158702100
+  version_requirements: *2166760100
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2158701520 !ruby/object:Gem::Requirement
+  requirement: &2166759620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +88,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2158701520
+  version_requirements: *2166759620
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2158700940 !ruby/object:Gem::Requirement
+  requirement: &2166759120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -99,10 +99,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2158700940
+  version_requirements: *2166759120
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2158700360 !ruby/object:Gem::Requirement
+  requirement: &2166758600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,7 +110,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2158700360
+  version_requirements: *2166758600
 description: Use the snp-search tool to create, import, manipulate and query your
   SNP database
 email: ali.al-shahib@hpa.org.uk
@@ -156,7 +156,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1150304421066674682
+      hash: -1735176367152600706
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: