cluster.rb in lederhosen-3.1.0

- old
+ new

@@ -2,26 +2,28 @@
 
   class CLI
 
     desc 'cluster', 'reference-based clustering using usearch'
 
-    method_option :input,    :type => :string,  :required => true
-    method_option :database, :type => :string,  :required => true
-    method_option :threads,  :type => :numeric, :default  => false
-    method_option :identity, :type => :numeric, :required => true
-    method_option :output,   :type => :string,  :required => true
-    method_option :strand,   :type => :string,  :default => 'plus'
-    method_option :dry_run,  :type => :boolean, :default => false
+    method_option :input,    :type  => :string,  :required => true
+    method_option :database, :type  => :string,  :required => true
+    method_option :threads,  :type  => :numeric, :default  => false
+    method_option :identity, :type  => :numeric, :required => true
+    method_option :output,   :type  => :string,  :required => true
+    method_option :strand,   :type  => :string,  :default  => 'plus'
+    method_option :dry_run,  :type  => :boolean, :default  => false
+    method_option :query_cov, :type => :numeric, :required => false, :default => 0.95
 
     def cluster
-      input    = File.expand_path(options[:input])
-      database = File.expand_path(options[:database])
-      threads  = options[:threads]
-      identity = options[:identity]
-      output   = File.expand_path(options[:output])
-      strand   = options[:strand]
-      dry_run  = options[:dry_run]
+      input     = File.expand_path(options[:input])
+      database  = File.expand_path(options[:database])
+      threads   = options[:threads]
+      identity  = options[:identity]
+      output    = File.expand_path(options[:output])
+      strand    = options[:strand]
+      dry_run   = options[:dry_run]
+      query_cov = options[:query_cov]
 
       ohai "#{'(dry run)' if dry_run} clustering #{input} to #{database} and saving to #{output}"
 
       options.each_pair do |key, value|
         ohai "#{key} = #{value}"
@@ -30,10 +32,11 @@
       cmd = ['usearch',
         "--usearch_local #{input}",
         "--id #{identity}",
         "--uc #{output}",
         "--db #{database}",
-        "--strand #{strand}"
+        "--strand #{strand}",
+        "--query_cov #{query_cov}"
       ]
 
       # threads = False : use all threads (default)
       if threads != false
         cmd << "--threads #{threads}"