bin/seqtrimnext in seqtrimnext-2.0.42 vs bin/seqtrimnext in seqtrimnext-2.0.45

@@ -263,10 +263,20 @@
 
   options[:json] = nil
   opts.on( '-j', '--json', 'Save results in json file' ) do
     options[:json] = true
   end
+  
+  options[:skip_output] = false
+  opts.on( '-K', '--no-verbose', 'Change to no verbose mode. Every sequence will not be written to output log' ) do
+    options[:skip_output] = true
+  end
+  
+  options[:skip_report] = false
+  opts.on( '-R', '--no-report', 'Change to no verbose mode. Every sequence will not be written to output log' ) do
+    options[:skip_report] = true
+  end
 
   # This displays the help screen, all programs are
   # assumed to have this option.
   opts.on_tail( '-h', '--help', 'Display this screen' ) do
     puts opts
@@ -298,11 +308,13 @@
 $LOG.datetime_format = "%Y-%m-%d %H:%M:%S"
 #logger.level = Logger::INFO
 
 #DEBUG < INFO < WARN < ERROR < FATAL < UNKNOWN
 
+$LOG.info("SeqTrimNext version #{Seqtrimnext::SEQTRIM_VERSION}")
 
+
 $LOG.info("Using BLASTDB: "+ $FORMATTED_DB_PATH)
 $LOG.info("Using options: "+ options.to_json)
 
 if options[:install_db] then
   #install databases
@@ -368,15 +380,22 @@
   exit
 end
 
 s = Seqtrim.new(options)
 
-#generate report
 
 
-if system("which generate_report.rb > /dev/null ")
+#generate report
+
+if !options[:skip_report] && system("which generate_report.rb > /dev/null ")
   cmd="generate_report.rb output_files 2> report_generation_errors.log"
   $LOG.info "Generating report #{cmd}"
   `#{cmd}`
 else
-  $LOG.info "If you want a detailed report in PDF format, install the optional seqtrimnext_report gem (gem install seqtrimnext_report)"
+  skip_text='.'
+  
+  if options[:skip_report]
+    skip_text=' and remove the -R option from the command line.'
+  end
+  
+  $LOG.info "If you want a detailed report in PDF format, be sure you have installed the optional seqtrimnext_report gem (gem install seqtrimnext_report)#{skip_text}"
 end