update analysis documentation-- especially "fingerprint"

[jeremymanning]

the API website here is out of date with the current version of quail. some of the inline documentation in the code itself is also out of date.

most of the inconsistencies won't lead to incorrect outputs, but one important update will be to correct how the "fingerprint" analysis says it runs by default vs. how it actually runs. the documentation (and comments in the code) say that the permutation version runs by default (with 1000 iterations), but in reality permutations are turned off by default (and they only run if you pass in permute=True).