[khmer] keep kmers stranded?

[C. Titus Brown]

On Wed, Jul 31, 2013 at 11:54:22AM +0200, Karl Nordstr?m wrote:
> Hi again,
> 
> I'm advancing by piecing together snippets from all the available scripts.
> One question though.
> 
> Does K have an upper limit? Loading a counting hash with K=31 and
> everything is fine, but with K=41 the following error appears:
> 
> python: ktable.cc:21: khmer::HashIntoType khmer::_hash(const char*,
> khmer::WordLength, khmer::HashIntoType&, khmer::HashIntoType&): Assertion
> `k <= sizeof(HashIntoType)*4' failed.
> Aborted
> 
> Or is this due to only using one strand? The code looked like a limitation.

Hi Karl, at the moment you can only go up to k=32.  Fixing this is rapidly
rising to the top of our stack -- it's not hard, just something we need to
do carefully.

cheers,
--titus

> On Mon, Jul 29, 2013 at 6:25 PM, C. Titus Brown <ctb at msu.edu> wrote:
> 
> > On Mon, Jul 29, 2013 at 05:35:13PM +0200, Karl Nordstr?m wrote:
> > > thank you very much. My intent was to write a simple filter with the help
> > > of the data structures, not anything fancy. Learn how to make use of this
> > > resource.
> > >
> > > I will try and see what happens.
> >
> > Cool -- let us know how it works out ;)
> >
> > cheers,
> > --titus
> >

-- 
C. Titus Brown, ctb at msu.edu