X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Ftrim_seq;h=c89eefb6d6ef95c18c0f89279a6370956e7d3874;hb=48bea5c28b89dc5586d0bddb338ccd6ba23aa1f9;hp=d6c1a0933dfe8a1dce77403c81414184d2f382bf;hpb=1db2127fa0928ad1531fc7f60d2dc1d497ee55b1;p=biopieces.git

diff --git a/bp_bin/trim_seq b/bp_bin/trim_seq
index d6c1a09..c89eefb 100755
--- a/bp_bin/trim_seq
+++ b/bp_bin/trim_seq
@@ -39,15 +39,17 @@ casts << {:long=>'trim',     :short=>'t', :type=>'string', :mandatory=>true, :de
 
 options = Biopieces.options_parse(ARGV, casts)
 
+trim = options[:trim].to_sym
+
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
-    if record.has_key? :SEQ and record.has_key? :SCORES
+    if record[:SEQ] and record[:SCORES]
       entry = Seq.new_bp(record)
 
-      case options[:trim]
-      when /both/  then entry.quality_trim!(options[:min_qual], options[:min_len])
-      when /left/  then entry.quality_trim_left!(options[:min_qual], options[:min_len])
-      when /right/ then entry.quality_trim_right!(options[:min_qual], options[:min_len])
+      case trim
+      when :both  then entry.quality_trim!(options[:min_qual], options[:min_len])
+      when :left  then entry.quality_trim_left!(options[:min_qual], options[:min_len])
+      when :right then entry.quality_trim_right!(options[:min_qual], options[:min_len])
       end
 
       record.merge! entry.to_bp