The sffToCA program converts 454 reads from SFF format to FRG. The logging could be better in CA 6.0.
1. Generate a clear audit, such that the sum of reads in each output category equals the total input.
2. Suppress alignment details. This was left on during recent debugging. This is making the log file too verbose.
3. If possible, reduce logging to one line per input read such that the full story is revealed by 'grep -c'.
4. Make sure the numbers add up. Currently, we see different total everywhere. Example:
removeDuplicateReads()-- from 1 to 588518
detectMates()-- from 1 to 588517