[khmer] khmer stripped header information from RNA-seq reads, rendering them unusable

[C. Titus Brown]

Hi all,

As a bottom line statement, I think it's clear that:

1) khmer should not generally be modifying sequence names;
2) where it does, it should explicitly say so;
3) where it's necessary, there should be warnings.
4) we should document all of this anyway, even though it's clear that
	most users don't read the docs :)

Sure, there are lots of hacks we can put in place but bitter experience
suggests that these will simply cause more problems in the long run.

--titus