snp-search 0.5.0 → 0.6.0

data/README.rdoc

@@ -16,17 +16,22 @@ To install snp-search, do
 
 * To run snp-search, you need to have 3 files:
 1- Variant Call Format (.vcf) file (which contains the SNP information)
+
 2- Your reference genome that you used to generate your .vcf file (in genbank or embl format, the script will automatically detect the format).
+
 3- A text file with a list of your strain/sample names.  These should be the same strains/samples used in generating the .vcf file. In the text file, every strain/sample name should have a new line, e.g.
 
+'''
 strain1
 strain2
 strain3
 strain4
 etc..
+'''
 
 * Once you have these files ready, you may run snp-search with the following options:
 
+'''
 -V	Enable verbose mode
 -n	Name of your database	Optional, default = snp_db.sqlite3
 -v	.vcf file	Required
@@ -35,6 +40,7 @@ etc..
 -c	SNP quality cuttoff.  A phred-scaled quality score. High quality scores indicate high confidence calls. Optional, default = 90
 -t	Genotype Quality cuttoff. This is the probability that the genotype call is wrong under the condition that the site is being variant.	Optional, default = 30
 -h	help message
+'''
 
 * Usage:
 snp-search -n my_snp_db.sqlite3 -r my_ref.gbk -v my_vcf_file.vcf -s my_list_of_strains.txt

data/VERSION

@@ -1 +1 @@
-0.5.0
+0.6.0

data/snp-search.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "snp-search"
-  s.version = "0.5.0"
+  s.version = "0.6.0"
 
   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: 0.5.0
+  version: 0.6.0
   prerelease: 
 platform: ruby
 authors:
@@ -14,7 +14,7 @@ date: 2011-12-01 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2158814260 !ruby/object:Gem::Requirement
+  requirement: &2154921840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2158814260
+  version_requirements: *2154921840
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2158813660 !ruby/object:Gem::Requirement
+  requirement: &2154921260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2158813660
+  version_requirements: *2154921260
 - !ruby/object:Gem::Dependency
   name: slop
-  requirement: &2158813060 !ruby/object:Gem::Requirement
+  requirement: &2154920680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2158813060
+  version_requirements: *2154920680
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2158812460 !ruby/object:Gem::Requirement
+  requirement: &2154920080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +55,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2158812460
+  version_requirements: *2154920080
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2158752880 !ruby/object:Gem::Requirement
+  requirement: &2154919480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2158752880
+  version_requirements: *2154919480
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2158752260 !ruby/object:Gem::Requirement
+  requirement: &2154918880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2158752260
+  version_requirements: *2154918880
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2158751780 !ruby/object:Gem::Requirement
+  requirement: &2154918300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2158751780
+  version_requirements: *2154918300
 description: Use the snp-search toolset to query the SNP database
 email: ali.al-shahib@hpa.org.uk
 executables:
@@ -130,7 +130,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2192451038165693366
+      hash: 2383223488984407940
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: