On 2017-05-04 12:14 (+0200), Michał J Gajda wrote:
> Interesting. Do You have an error report filed anywhere to peruse?
Well, I wrote the below. In the mean time, I've tried replacing
"insertWith" with a manual lookup and update. This changed the cases
where the segfaults happen, but didn't e
> What is the ratio of used/unused keys in the final associative
> structure? That is, how many k-mers do you expect not to exist in your
> DNA sequence? Maybe one could pre-compress the key set by knowing
> which k-1-mers exist, then use a simple Vector, accepting some space
> wasted?
Perhaps i
Sorry for the late answer - but "bio" is deprecated these days, you
should use biofasta (and biocore, etc) instead.
(Note that you may have to get it off GitHub rather than with
cabal-install, I'm afraid I've been lazy about pushing updates in that
direction lately.)
-k
On 2017-03-21 15:50 (+01
Ketil,
Given that the dump looks fine, my gut feeling is that indeed the histogram
function operates on partially evaluated data and somehow the memory is
corrupted. Can you write a Deepseq instance for your Judy array? After all, you
could dump to a [(String,Int)] instead of an IO handle and
> Am 09.05.2017 um 09:38 schrieb Ketil Malde :
>
>
>> What is the ratio of used/unused keys in the final associative
>> structure? That is, how many k-mers do you expect not to exist in your
>> DNA sequence? Maybe one could pre-compress the key set by knowing
>> which k-1-mers exist, then use a
