How to log bug reports for cortex_var

software for genome assembly and variation analysis

If you find cortex_var is behaving not according to expectations and want to report a bug, then please reproduce the bug one more time with debugging turned on (explained below) and log a bug report as follows:

  1. Recompile cortex with debugging turned on. First type make clean, then add DEBUG=1 to your compile command. For example, if your command previously was for 2-colour cortex, with k<32, then type make DEBUG=1 NUM_COLS=2 cortex_var.
  2. Type gdb cortex_var_31_c2 (replace _31_c2 with whatever is appropriate for your case)
  3. Suppose the command that caused the problem was cortex_var_31_c2 --kmer_size 21 --mem_height 17 --mem_width 100 --multicolour_bin blah ..other options. Then type run --kmer_size 21 --mem_height 17 --mem_width 100 --multicolour_bin blah ..other options.
  4. Now wait until the bug happens. Then type bt and copy-paste the ALL of the output (everything you typed, and everything that was output) into a text file.
  5. Right click on this link and open it in a new window or tab (so you can continue to refer back to these instructions).
  6. Click on Tracker, which generates a drop-down list, and then click on Bugs
  7. Click on Add new, set the Category to cortex_var. Don't worry about Group, AssignTo or Priority. Give the bug report a descriptive title in the Summary box, and then describe your problem in the Description box. Then paste the contents of the text file you have saved in the description box (or upload it using the UploadFile button)
  8. Click on Add Artifact, and you have finished your bug report! Thanks very much for your help - this is much appreciated.