fixed seq qual length check

[biopieces.git] / bp_bin / shuffle_records

diff --git a/bp_bin/shuffle_records b/bp_bin/shuffle_records
index b13222956b797c5fd04ed5605cc1ff7e34ab3edf..ae62a3108df6cf913cf116ac5598d6b2787598cc 100755 (executable)
--- a/bp_bin/shuffle_records
+++ b/bp_bin/shuffle_records
@@ -29,22 +29,20 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-require 'biopieces'
+require 'maasha/biopieces'
 
-casts = []
-
-bp = Biopieces.new
-
-options = bp.parse(ARGV, casts)
+options = Biopieces.options_parse(ARGV)
 
 records = []
 
-bp.each_record do |record|
-  records << record
-end
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    records << record
+  end
 
-records.shuffle.each do |record|
-  bp.puts record
+  records.shuffle.each do |record|
+    output.puts record
+  end
 end