fixed seq qual length check

[biopieces.git] / bp_bin / bin_vals

diff --git a/bp_bin/bin_vals b/bp_bin/bin_vals
index 42fb7d6869eeecdec7af9412c50189ff18772338..a0bad392a8c6f6bb58499e3d9f5b11ebabc7db17 100755 (executable)
--- a/bp_bin/bin_vals
+++ b/bp_bin/bin_vals
@@ -29,22 +29,22 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-require 'biopieces'
+require 'maasha/biopieces'
 
 casts = []
 casts << {:long=>'key',      :short=>'k', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'bin_size', :short=>'b', :type=>'uint',   :mandatory=>true, :default=>10,  :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_record do |record|
+    if record[options[:key].to_sym]
+      record[(options[:key] + "_BIN").to_sym] = (record[options[:key].to_sym].to_i / options[:bin_size]) * options[:bin_size]
+    end
 
-bp.each_record do |record|
-  if record.has_key? options[:key]
-    record[(options[:key].to_s + "_BIN").to_sym] = (record[options[:key]].to_i / options[:bin_size]) * options[:bin_size]
+    output.puts record
   end
-
-  bp.puts record
 end