refactoring of assemble_pairs

[biopieces.git] / bp_bin / progress_meter

diff --git a/bp_bin/progress_meter b/bp_bin/progress_meter
index b5e0c1c53e9288b45425b4ffc8ba6c049887ad60..43cdd771d0b8e38d1d5733e83404082fde78d310 100755 (executable)
--- a/bp_bin/progress_meter
+++ b/bp_bin/progress_meter
@@ -29,23 +29,24 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-require 'biopieces'
+require 'maasha/biopieces'
 
 casts = []
 casts << {:long=>'no_stream', :short => 'x', :type => 'flag', :mandatory => false, :default => nil,  :allowed => nil, :disallowed => nil}
 casts << {:long=>'count',     :short => 'c', :type => 'uint', :mandatory => false, :default => 1000, :allowed => nil, :disallowed => '0'}
 
-bp = Biopieces.new
+options = Biopieces.options_parse(ARGV, casts)
 
-options = bp.parse(ARGV, casts)
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_with_index do |record, count|
+    output.puts record unless options[:no_stream]
+    $stderr.printf "\n% 9d ", count if (count % (options[:count] * 100)) == 0
+    $stderr.print "." if (count % options[:count]) == 0
+  end
 
-bp.each_with_index do |record, count|
-  bp.puts record unless options.has_key? :no_stream
-  $stderr.printf "\n% 9d ", count if (count % (options[:count] * 100)) == 0
-  $stderr.print "." if (count % options[:count]) == 0
+  $stderr.puts
 end
 
-$stderr.puts
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<