bin/split_fastq.rb in seqtrimnext-2.0.57 vs bin/split_fastq.rb in seqtrimnext-2.0.59

@@ -2,23 +2,29 @@
 
 require 'scbi_fastq'
 
 
 if ARGV.count < 3
-  puts "#{$0} FASTQ OUTPUT_NAME SPLIT_BY"
+  puts "#{$0} FASTQ OUTPUT_NAME SPLIT_BY [-gz]"
   exit
 end
 
-
   
 fastq = ARGV.shift
 output_name = ARGV.shift
 split_by = ARGV.shift.to_i
 
+gz_arg=ARGV.shift
+gz=false
 
+if !gz_arg.nil? and gz_arg.index('-gz')
+	gz='.gz'
+end
+
+
 file_index=1
-out=FastqFile.new("#{output_name}#{file_index}.fastq",'w')
+out=FastqFile.new("#{output_name}#{file_index}.fastq#{gz}","w#{gz}")
 
 fqr=FastqFile.new(fastq)
 
 count = 0
 
@@ -30,10 +36,10 @@
 
   if (count % split_by) == 0 
       
     file_index +=1
     out.close
-    out=FastqFile.new("#{output_name}#{file_index}.fastq",'w')
+    out=FastqFile.new("#{output_name}#{file_index}.fastq#{gz}","w#{gz}")
 
   end
 end
 
 out.close