seqtrimnext 2.0.56 → 2.0.57

checksums.yaml

@@ -1,7 +1,7 @@
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data/History.txt

@@ -1,3 +1,7 @@
+=== 2.0.57 2013-07-26
+
+Option to disable reject by vectors in the middle
+
 === 2.0.56 2013-07-25
 
 added split_fasta.rb script

data/lib/seqtrimnext.rb

@@ -30,7 +30,7 @@ module Seqtrimnext
   # SEQTRIM_VERSION_STAGE = 'b'
   # SEQTRIM_VERSION = "2.0.0#{SEQTRIM_VERSION_STAGE}#{SEQTRIM_VERSION_REVISION}"
   
-   VERSION = '2.0.56'
+   VERSION = '2.0.57'
   
   SEQTRIM_VERSION = VERSION
   

data/lib/seqtrimnext/plugins/plugin_vectors.rb

@@ -110,8 +110,10 @@ class PluginVectors < Plugin
          if !near_to_extrem(v,seq,min_vector_size)
        		type = 'ActionUnexpectedVector'
 
-    			  seq.seq_rejected=true 
-				  seq.seq_rejected_by_message='unexpected vector'
+          if @params.get_param('middle_vector_rejects')=='true'
+    			  seq.seq_rejected=true
+  				  seq.seq_rejected_by_message='unexpected vector'
+          end
 				  
 				  add_stats('rejected','unexpected_vector')
 
@@ -171,6 +173,11 @@ class PluginVectors < Plugin
 		default_value = File.join($FORMATTED_DB_PATH,'vectors.fasta')
 		params.check_param(errors,'vectors_db','DB',default_value,comment)
 
+    comment='Rejects sequences with vectors in the middle'
+    default_value = 'true'
+    params.check_param(errors,'middle_vector_rejects','String',default_value,comment)
+
+
     # params.split_databases('vectors_db')
     
     return errors

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: seqtrimnext
 version: !ruby/object:Gem::Version 
-  version: 2.0.56
+  version: 2.0.57
 platform: ruby
 authors: 
 - Dario Guerrero & Almudena Bocinos
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2013-07-25 00:00:00 Z
+date: 2013-07-26 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: narray