snp-search 0.6.0 → 0.7.0

data/README.rdoc

@@ -10,41 +10,41 @@ To install snp-search, do
 
 == Requirements
 
-* Nothing! You just need to run this in unix and it will install all the necessary gems for you.
+Nothing! You just need to run this in unix and it will install all the necessary gems for you.
 
 == Running snp-search   
 
-* To run snp-search, you need to have 3 files:
+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
--r	Reference genome file (The same file that was used in generating the .vcf file).  This should be in genbank or embl format.	Required
--s	Text file that contains a list of the strain/sample names (The same strains/samples used in generating the .vcf file)	Required
--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:
+  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
+  -r	Reference genome file (The same file that was used in generating the .vcf file).  This should be in genbank or embl format.	Required
+  -s	Text file that contains a list of the strain/sample names (The same strains/samples used in generating the .vcf file)	Required
+  -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
 
+Have fun snp-searching!
+
 == Copyright
 
 Copyright (c) 2011 Ali Al-Shahib. See LICENSE.txt for

data/VERSION

@@ -1 +1 @@
-0.6.0
+0.7.0

data/snp-search.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "snp-search"
-  s.version = "0.6.0"
+  s.version = "0.7.0"
 
   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: 0.6.0
+  version: 0.7.0
   prerelease: 
 platform: ruby
 authors:
@@ -14,7 +14,7 @@ date: 2011-12-01 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2154921840 !ruby/object:Gem::Requirement
+  requirement: &2158814220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2154921840
+  version_requirements: *2158814220
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2154921260 !ruby/object:Gem::Requirement
+  requirement: &2158813620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2154921260
+  version_requirements: *2158813620
 - !ruby/object:Gem::Dependency
   name: slop
-  requirement: &2154920680 !ruby/object:Gem::Requirement
+  requirement: &2158813020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2154920680
+  version_requirements: *2158813020
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2154920080 !ruby/object:Gem::Requirement
+  requirement: &2158812420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +55,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2154920080
+  version_requirements: *2158812420
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2154919480 !ruby/object:Gem::Requirement
+  requirement: &2158752840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2154919480
+  version_requirements: *2158752840
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2154918880 !ruby/object:Gem::Requirement
+  requirement: &2158752260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2154918880
+  version_requirements: *2158752260
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2154918300 !ruby/object:Gem::Requirement
+  requirement: &2158751780 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2154918300
+  version_requirements: *2158751780
 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: 2383223488984407940
+      hash: -491927113428014191
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: