rewrote assemble_seq_velvet

[biopieces.git] / bp_bin / read_fastq

diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
index acc68d653fccf1ed40e662df20840407d6fca3db..c2f74cd7bb7a07219ac43ecfd574ad726f5b8f00 100755 (executable)
--- a/bp_bin/read_fastq
+++ b/bp_bin/read_fastq
@@ -44,7 +44,7 @@ num  = 0
 last = false
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-  unless options[:data_in].first == '-'
+  unless options[:data_in] and options[:data_in].first == '-'
     input.each_record do |record|
       output.puts record
     end
@@ -57,9 +57,9 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
       Fastq.open(file, mode='r') do |fastq|
         fastq.each do |entry|
           if encoding == 'auto'
-            if entry.qual.match(/[!-:]/) # sanger or illumina18
+            if entry.qual_base33? # sanger or illumina18
               encoding = 'illumina18'
-            elsif entry.qual.match(/[K-h]/) # solexa or illumina13 or illumina15
+            elsif entry.qual_base64? # solexa or illumina13 or illumina15
               encoding = 'illumina13'
             else
               raise SeqError, "Could not auto-detect quality score encoding"