Re: [Denovoassembler-devel] RE : RE : Why flush both k-mer and its complement?

[David E. (gringer) <dav...@mp...>]

On 21/07/11 17:56, Sébastien Boisvert wrote:
> So basically, if your patch is modified to flush the lowest k-mer among a and b, then it should work fine.

Attached. Note that this is actually 2 reverse-complements, not 1, 
because a reverse-complement is needed in order to get the correct 
vertex rank. I suppose you could avoid this by modifying the vertex rank 
function to take a boolean "actually, don't bother with finding the 
lowest k-mer, I've already done that."

oh... and looking at the vertexRank function, you could eliminate a Kmer 
copy by using an if statement (see attached patch, which does both of 
these things, but doesn't modify the KmerAcademyBuilder.cpp function to 
take advantage of that).

FWIW, when I run this (both patches applied) on my phiX_5k data, it 
produces different coverage distributions each time. Does this make sense?

-- David