fixed quality score validity check

[biopieces.git] / bp_bin / read_fastq

diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
index 44a69ed871cd40f686d4f9be675258377b4c6ebf..96be2c3a06f8b2762fdfa3e918fe68f091c74fce 100755 (executable)
--- a/bp_bin/read_fastq
+++ b/bp_bin/read_fastq
@@ -65,12 +65,15 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
             else
               raise SeqError, "Could not auto-detect quality score encoding"
             end
-          elsif first
-            #raise SeqError, "Quality score outside valid range" unless entry.qual_valid?(encoding)
-            first = false
           end
 
           entry.convert_scores!(encoding, 'illumina13')
+
+          if first
+            raise SeqError, "Quality score outside valid range" unless entry.qual_valid?('illumina13')
+            first = false
+          end
+
           output.puts entry.to_bp
           num += 1