changed trim_seq to omit outputting sequences with length 0

[biopieces.git] / bp_scripts / QA_454_report.rb

diff --git a/bp_scripts/QA_454_report.rb b/bp_scripts/QA_454_report.rb
index 1201389ea785e4fa881f189f1c6af2461c20504c..37da5beb30a81655b4f3bf1a6275ccfc70b874cf 100755 (executable)
--- a/bp_scripts/QA_454_report.rb
+++ b/bp_scripts/QA_454_report.rb
@@ -130,13 +130,13 @@ class Report
     def bp_plot
       STDERR.puts "Creating plots ... "
       system(
-        "read_sff -c -i #{@sff_file} |
+        "read_sff -m -i #{@sff_file} |
          progress_meter |
          plot_distribution -k SEQ_LEN -T 'Length Distribution - unclipped' -t png -o #{@plot1} |
-         plot_scores -T 'Mean Quality Scores - unclipped' -t png -o #{@plot2} |
+         plot_scores -c -T 'Mean Quality Scores - unclipped' -t png -o #{@plot2} |
          clip_seq |
          plot_distribution -k SEQ_LEN -T 'Length Distribution - clipped' -t png -o #{@plot3} |
-         plot_scores -T 'Mean Quality Scores - clipped' -t png -o #{@plot4} |
+         plot_scores -c -T 'Mean Quality Scores - clipped' -t png -o #{@plot4} |
          mean_scores |
          bin_vals -k SCORES_MEAN -b 5 |
          plot_histogram -s num -k SCORES_MEAN_BIN -T 'Mean score bins' -X 'Bins (size 5)' -Y 'Count' -t png -o #{@plot5} -x"