bin/seqtrimnext in seqtrimnext-2.0.46 vs bin/seqtrimnext in seqtrimnext-2.0.48

@@ -204,10 +204,15 @@
 
   options[:check_db] = false
   opts.on( '-c', '--check_databases', 'Check Blast databases and reformat if necessary' ) do
     options[:check_db] = true
   end
+
+  options[:use_checkpoint] = false
+  opts.on( '-C', '--use_checkpoint', 'Restore at checkpoint if scbi_mapreduce_checkpoint file is available' ) do
+    options[:use_checkpoint] = true
+  end
   
   # options[:skip_initial_stats] = false
   # opts.on( '-k', '--skip_initial_stats', 'Skip initial stats' ) do
   #   options[:skip_initial_stats] = true
   # end
@@ -225,9 +230,19 @@
 
   options[:fastq] = nil
   opts.on( '-Q', '--fastq FILE', 'Fastq input file. Use - for <STDIN>' ) do |file|
     options[:fastq] = file
   end
+  
+  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
+    end
+  end
+  
 
   options[:fasta] = nil
   opts.on( '-f', '--fasta FILE', 'Fasta input file' ) do |file|
     options[:fasta] = file
   end