vardetect-vc 0.0.2 → 0.0.3

data/lib/vardetect-vc.rb

@@ -1,7 +1,66 @@
 require "vardetect-vc/version"
+require "vardetect-vc/lib"
+require 'ffi'
+require "bio/db/sam"
+require "bio/db/sam/sam"
+require "bio/db/pileup"
+require "bio/db/vcf"
+
+# tasks :
+# 1. include indel mutation detection
+# 2. include base call quality        =>    completed
+# 3. recalling 
+# 4. known snp
+# 5. snv function
+# 6. interactive 
+# 7. workflow
 
 module Vardetect
   module Vc
-    # Your code goes here...
+    def self.hi
+      puts 'hello inside '
+    end
+    
+    # command params options
+    # variance call
+    def self.exec args
+      params = parse_params args.join(' ')
+      puts params.inspect
+      
+      cmd = params[:cmd]
+
+      case cmd
+        
+      when 'snv'
+
+        call_snv params
+        
+      when 'snv-range'
+
+        call_snv_range params
+
+      when 'prepare-st'
+
+        call_prepare_st params
+
+      when 'prepare-snp'
+
+        call_prepare_snp params
+
+      when 'prepare-vc'
+
+        call_prepare_vc params
+
+      when 'combine-all'
+
+        call_combine_all params
+
+      when 'analyse-combine'
+
+        call_analyse_combine params
+        
+      end
+      
+    end
   end
 end

data/lib/vardetect-vc/version.rb

@@ -1,5 +1,5 @@
 module Vardetect
   module Vc
-    VERSION = "0.0.2"
+    VERSION = "0.0.3"
   end
 end

data/vardetect-vc.gemspec

@@ -13,11 +13,12 @@ Gem::Specification.new do |gem|
   gem.homepage      = ""
   gem.files         = `git ls-files`.split($/)
   gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.default_executable = 'bin/vardetect-vc'
   gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
   gem.require_paths = ["lib"]
   
-  gem.add_development_dependency "bio-samtools"
   gem.add_development_dependency "ffi"
+  gem.add_development_dependency "bio-samtools"
   gem.add_runtime_dependency "ffi"
   gem.add_runtime_dependency "bio-samtools"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vardetect-vc
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,10 +9,10 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-11-19 00:00:00.000000000 Z
+date: 2012-11-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: bio-samtools
+  name: ffi
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
@@ -28,7 +28,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: ffi
+  name: bio-samtools
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements: