snp-search 0.32.0 → 0.33.0

data/README.rdoc

@@ -38,6 +38,8 @@ Once you have these files ready, you may run snp-search with the following optio
 Usage:
   snp-search -n my_snp_db.sqlite3 -d my_ref.gbk -v my_vcf_file.vcf 
 
+Note: The strain names in your database will be taken from your vcf file so make sure they are named appropriately in your vcf file.
+
 == Output
 The output is your database in sqlite3 format.  If you like to view your table(s) and perform queries you can type 
   sqlite3 snp_db.sqlite3

data/VERSION

@@ -1 +1 @@
-0.32.0
+0.33.0

data/lib/snp-search.rb

@@ -56,7 +56,7 @@ puts "Adding SNPs........"
 	  # header names
 		while line = f.gets
 	  		if  line =~ /CHROM/
-	  			line.chomp
+	  			line.chomp!
 				column_headings = line.split("\t")
 				strain_names = column_headings[9..-1]
 				strain_names.map!{|name| name.sub(/\..*/, '')}

data/snp-search.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "snp-search"
-  s.version = "0.32.0"
+  s.version = "0.33.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ali Al-Shahib", "Anthony Underwood"]
-  s.date = "2012-01-09"
+  s.date = "2012-01-11"
   s.description = "Use the snp-search tool to create, import, manipulate and query your SNP database"
   s.email = "ali.al-shahib@hpa.org.uk"
   s.executables = ["snp-search"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: snp-search
 version: !ruby/object:Gem::Version
-  version: 0.32.0
+  version: 0.33.0
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-09 00:00:00.000000000Z
+date: 2012-01-11 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2168842620 !ruby/object:Gem::Requirement
+  requirement: &2158704900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: 3.1.3
   type: :runtime
   prerelease: false
-  version_requirements: *2168842620
+  version_requirements: *2158704900
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2168842040 !ruby/object:Gem::Requirement
+  requirement: &2158704300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -33,10 +33,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2168842040
+  version_requirements: *2158704300
 - !ruby/object:Gem::Dependency
   name: slop
-  requirement: &2168841440 !ruby/object:Gem::Requirement
+  requirement: &2158703720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -44,10 +44,10 @@ dependencies:
         version: 2.4.0
   type: :runtime
   prerelease: false
-  version_requirements: *2168841440
+  version_requirements: *2158703720
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2168840820 !ruby/object:Gem::Requirement
+  requirement: &2158703220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +55,10 @@ dependencies:
         version: 1.3.4
   type: :runtime
   prerelease: false
-  version_requirements: *2168840820
+  version_requirements: *2158703220
 - !ruby/object:Gem::Dependency
   name: activerecord-import
-  requirement: &2168839800 !ruby/object:Gem::Requirement
+  requirement: &2158702700 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 0.2.8
   type: :runtime
   prerelease: false
-  version_requirements: *2168839800
+  version_requirements: *2158702700
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2168839320 !ruby/object:Gem::Requirement
+  requirement: &2158702100 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2168839320
+  version_requirements: *2158702100
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2168838760 !ruby/object:Gem::Requirement
+  requirement: &2158701520 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +88,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2168838760
+  version_requirements: *2158701520
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2168838280 !ruby/object:Gem::Requirement
+  requirement: &2158700940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -99,10 +99,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2168838280
+  version_requirements: *2158700940
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2168837800 !ruby/object:Gem::Requirement
+  requirement: &2158700360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,7 +110,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2168837800
+  version_requirements: *2158700360
 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: 4420329220307997884
+      hash: 1150304421066674682
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: