cagnut_bwa 0.3.1 → 0.3.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  metadata.gz: 9a590ef059a51b29608fa778fb7240b15fd35324
-  data.tar.gz: 84eb55f1953dee48a355399b869b93dca3ae2eda
+  metadata.gz: 97a5d23cc8316d1b59b094e87e31d8ee1aac2308
+  data.tar.gz: 0b79d3b340ddb09a6c0d685e70d4f0a679cffecf
 SHA512:
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+  metadata.gz: ec0ef694d43675ba5e27548d63ab818e0fe57c1b574ffae58648a19da42fe84266fb2d0222ada1437c9f7b5ee59cac680e2ba4bde5c84cd4c96b4164cf28157e
+  data.tar.gz: c36780081df3e223280c5ac07c917432df5b131f955cd5885d2c82a575850cafe7d2c0eb609b086158f18b5154f5a4d4df0a6b88f2c160998255e403e0071dda

data/lib/cagnut_bwa/check_tools.rb

@@ -1,26 +1,24 @@
 module CagnutBwa
   module CheckTools
-    def check_tool tools_path
+    def check_tool tools_path, refs=nil
       super if defined?(super)
-      check_bwa tools_path['bwa']
-      check_bwa_index refs['ref_fasta']
+      ver = check_bwa tools_path['bwa'], refs['ref_fasta']
+      check_bwa_index tools_path['bwa'], refs['ref_fasta'] if ver.blank?
     end
 
-    def check_bwa path
+    def check_bwa path, ref_path
       check_tool_ver 'BWA' do
         `#{path} 2>&1 | grep Version | cut -f2 -d ' '` if path
-        check_bwa_index
       end
     end
 
-    def check_bwa_index ref_path
+    def check_bwa_index tool_path, ref_path
       tool = 'Bwa Index'
       file = "#{ref_path}.ann"
-      command = "#{@config['tools']['bwa']} index #{ref_path}"
+      command = "#{tool_path} index #{ref_path}"
       check_ref_related file, tool, command
     end
 
-
     def check_ref_related file, tool, command
       if File.exist?(file)
         puts "\t#{tool}: Done"

data/lib/cagnut_bwa/version.rb

@@ -1,3 +1,3 @@
 module CagnutBwa
-  VERSION = "0.3.1"
+  VERSION = "0.3.2"
 end

data/lib/cagnut_bwa.rb

@@ -12,5 +12,6 @@ module CagnutBwa
 end
 
 require 'cagnut_bwa/configuration'
+require 'cagnut_bwa/check_tools'
 require 'cagnut_bwa/base'
 require 'cagnut_bwa/util'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cagnut_bwa
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.3.2
 platform: ruby
 authors:
 - Shi-Gang Wang