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