Comparing two sketches constructed from --parse-by-seq

[Malfoy]

Let's say I build two sketches like this

dashing2 sketch --parse-by-seq ecoli1.fa -o ecoli1
dashing2 sketch --parse-by-seq ecoli1.fa -o ecoli2

If I try to compare both sketches containing a lot of sequences I obtain this very small matrix.

dashing2 cmp ecoli1 ecoli2
#Dashing2 Symmetric pairwise Output
#Dashing2Options: Dashing2Options;k:32;parsebyfile;trimchr;sketchsize:1024;sketchtype:onepermsetsketch;Fastx;canon
#Sources ecoli1 ecoli2
ecoli1 - 1
ecoli2 - -

How can I actually perform the all versus all comparison ?

Thank you for your help!

[dnbaker]

Hi -

You should be able to compare using "--presketched" when calling cmp. Let me know if that doesn't work.

Thanks!

Daniel

[Malfoy]

Can you give me a sample command line ?
In a simpler example:

dashing2 sketch -k 31 -p 63 -S1000 -F fof1.txt -o sketch1;
dashing2 sketch -k 31 -p 63 -S1000 -F fof2.txt -o sketch2;

dashing2 cmp --presketched sketch1 sketch2;
give me terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr: __pos (which is 18446744073709551615) > this->size() (which is 8)
[1] 1936556 IOT instruction (core dumped) dashing2 cmp --presketched sketch1 sketch2