		     1001 Ways to Make COP Better
				   
			      Simon Dear
			   3 December 1991
				   

1. Incorporate quality considerations.
Certain problems can slip through the detetion net. An example are
overcalled bases in the consensus. Currently the whole raw data read
is used, and overcalling will agree with the consensus. Overcalled
runs of bases are very symptomatic of poor trace quality. If these
could be detected and excluded from the coverage map, the problem
would be detected.

2. Running the program on contigs and regions of contigs.
Cop could then be run on partially completed project databases.

3. Provide explanations as to why a region is problematic.
Maybe this isn't worth the effort to implement, but would be useful.

4. Take into account strandedness.
This would help detect regions where the coverage by good quality
traces is poor.

5. Interface to contig editor.
The contig editor could center on and highlight regions where problems
exist, speeding up the process.

6. Consensus coverage.
Currently if 10 good readings disagree with a region and just 1
mediocre reading agrees, no problem is detected.

7-1001. Make it detect 995 times as many problems.
