max kmer for single pass diginorm

[macmanes]

I'm trying to do a classroom experiment using smaller and larger values for k.It looks like kmer=31 is the largest possible size, but why is this so? Also, the error message for kmer sizes > 31 could be more clear.

normalize-by-median.py -p -x 15e8 -k 33 -C 50 --out khmer_normalized.fq interleaved.fq

|| This is the script 'normalize-by-median.py' in khmer.
|| You are running khmer version 1.2-rc2-6-gc5dee21
|| You are also using screed version 0.7
||
|| If you use this script in a publication, please cite EACH of the following:
||
||   * MR Crusoe et al., 2014. doi: 10.6084/m9.figshare.979190
||   * CT Brown et al., arXiv:1203.4802 [q-bio.GN]
||
|| Please see http://khmer.readthedocs.org/en/latest/citations.html for details.
PARAMETERS:
 - kmer size =    33        (-k)
 - n tables =     4         (-N)
 - min tablesize = 1.5e+09  (-x)
Estimated memory usage is 6e+09 bytes (n_tables x min_tablesize)
--------
making k-mer counting table
terminate called after throwing an instance of 'khmer::khmer_exception'
  what():  Supplied kmer string doesn't match the underlying k-size.
Aborted (core dumped)

[ctb]

On Thu, Oct 23, 2014 at 05:55:41PM -0700, Matt MacManes wrote:

I'm trying to do a classroom experiment using smaller and larger values for k.It looks like kmer=31 is the largest possible size, but why is this so? Also, the error message for kmer sizes > 31 could be more clear.

Thanks, Matt!

The k-mer size implementation is pleiotropic; @wrightmhw is working to fix.
For now we're limited to 64 bits or 32 bases of DNA.

Agreed on error message :).

best,
--titus

[ctb]

ksize upgrade in #624; core issue is #60. Punted error message fix to #1094.