vardetect-vc 0.0.3 → 0.0.4

data/README.md

@@ -27,3 +27,11 @@ TODO: Write usage instructions here
 3. Commit your changes (`git commit -am 'Add some feature'`)
 4. Push to the branch (`git push origin my-new-feature`)
 5. Create new Pull Request
+
+156553003
+156571176
+
+
+168665645
+
+170706648

data/lib/vardetect-vc.rb

@@ -34,6 +34,31 @@ module Vardetect
       when 'snv'
 
         call_snv params
+      
+      when 'snv-batch'  
+        
+        path = '/Users/soup/Desktop/chula/data'
+        path = params['path'] if params['path']
+       
+        working = params['exp']
+        
+        for i in params['samples'].split(',').compact
+        
+        sample_id = i
+        
+        
+        ref_file = File.join(path,'ref','hg19.fa')
+        sam_file = File.join(path,working,'bam',"#{sample_id}.remdup.uniqMap.TS.bam")
+        vc_raw_file = File.join(path,working,'snv-vc',"#{sample_id}_vc_raw_snv.tsv")
+        
+        p = "snv -ref #{ref_file} -sam #{sam_file} -vc_out #{vc_raw_file} -core 16"
+        
+        p = parse_params(p)
+        puts p.inspect
+          call_snv p
+        
+        end
+        
         
       when 'snv-range'
 

data/lib/vardetect-vc/version.rb

@@ -1,5 +1,5 @@
 module Vardetect
   module Vc
-    VERSION = "0.0.3"
+    VERSION = "0.0.4"
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vardetect-vc
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-11-20 00:00:00.000000000 Z
+date: 2012-11-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi