Hash collision rate may be higher than it ought to be

[rsharris]

(All of the following is hypothetical work, but there is currently no plan to do this.)

Canonicalization of the hash function by using h(forward)+h(revcomp) may be introducing more collisions. The solution would be to use something like min(h(forward),(revcomp)), though this can skew the distribution of bits.

More testing would be needed to determine whether the current canonicalization is really a problem.

If it is a problem, any solution needs to retain backward compatibility so as to insure compatibility with existing files. The BF file format includes a version number -- newer versions of the program would recognize the earlier file versions and use the current hash function with those. Newly created BF files would use the new hash function. Older versions of the program would reject the new files.