rewrite of FASTQ internals

[biopieces.git] / bp_bin / assemble_pairs

diff --git a/bp_bin/assemble_pairs b/bp_bin/assemble_pairs
index 440810b23f5f7fb7b400f09c71af3c6126ed3295..c9e0eb09c2b3eebe8fa58c8f32bfa0f426b17f47 100755 (executable)
--- a/bp_bin/assemble_pairs
+++ b/bp_bin/assemble_pairs
@@ -87,7 +87,6 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   io_in2.close
 
   cmd = "pandaseq"
-  cmd << " -6"
   cmd << " -F"
   cmd << " -B"
   cmd << " -N"
@@ -105,7 +104,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 
   Fastq.open(file_out) do |ios|
     ios.each do |entry|
-      output.puts entry.convert_scores!('illumina18', 'illumina15').to_bp
+      output.puts entry.to_bp
     end
   end
 end