seqtrimnext in seqtrimnext-2.0.66

- old
+ new

@@ -214,11 +214,11 @@
     else
       begin
         options[:workers] = Integer(workers)
       rescue
         STDERR.puts "ERROR:Invalid workers parameter #{options[:workers]}"
-        exit
+        exit -1
       end
 
     end
 
   end
@@ -266,11 +266,11 @@
   options[:format] = nil
   opts.on( '-F', '--fastq_quality_format FORMAT', 'Fastq input quality format use sanger or illumina18 for phred+33 based scores. Use illumina15 for phred+64 based scores (default is sanger) file. Use - for <STDIN>' ) do |value|
     options[:format] = value
     if !['sanger','illumina15', 'illumina18'].include?(value)
       STDERR.puts "ERROR: Invalid FASTQ format parameter #{value}"
-      exit
+      exit -1
     end
   end
 
 
   options[:fasta] = nil
@@ -299,11 +299,11 @@
   options[:template] = nil
   opts.on( '-t', '--template TEMPLATE_FILE', 'Use TEMPLATE_FILE instead of default parameters' ) do |file|
     options[:template] = file
   end
 
-  options[:chunk_size] = 100
+  options[:chunk_size] = 5000
   opts.on( '-g', '--group_size chunk_size', 'Group sequences in chunks of size <chunk_size>' ) do |cs|
     options[:chunk_size] = cs.to_i
   end
 
 
@@ -330,27 +330,27 @@
   # This displays the help screen, all programs are
   # assumed to have this option.
   opts.on_tail( '-h', '--help', 'Display this screen' ) do
     puts opts
     show_additional_help
-    exit
+    exit -1
   end
 end
 
 # parse options and remove from ARGV
 optparse.parse!
 
 if options[:list_db] then
   # List database entries in a database
   ListDb.new($DB_PATH,options[:list_db_name])
-  exit
+  exit -1
 end
 
 if options[:gen_params] then
   # Generates a sample params file in current directory
   Params.generate_sample_params
-  exit
+  exit -1
 end
 
 #set logger
 # system('rm logs/*')
 FileUtils.mkdir('logs') if !File.exists?('logs')
@@ -451,5 +451,7 @@
     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
+
+exit(Seqtrim.exit_status)