Parsing lowercase and unknown characters.

[GordonHoklinder]

fixes #7

[karel-brinda]

Just a quick comment – it would be good to always use meaningful names of PRs – when ppl are managing multiple projects, it's always difficult to remember ids of issues and PRs across repos (e.g, what's under the number 7 in this case :))

[karel-brinda]

(also the same for branch names – it's really helpful when the name can be easily associated with the bug – in this case, it could be eg nonamb-nucl or something like that)

[karel-brinda]

I'm currently getting some unexpected results.

$ ./kmers -p ~/github/my/rase-db-spneumoniae-sparc/isolates/001334.fa -k31 > output.fa 
$ l output.fa 
-rw-r--r--  1 karel  staff   157K Nov  5 23:49 output.fa

I.e., the output file is too small (but it doesn't fail anymore).

[GordonHoklinder]

Just a quick comment – it would be good to always use meaningful names of PRs – when ppl are managing multiple projects, it's always difficult to remember ids of issues and PRs across repos (e.g, what's under the number 7 in this case :))

Yes, it was probably too late for me to notice that I left there the default name. o:-)

[GordonHoklinder]

I'm currently getting some unexpected results.

$ ./kmers -p ~/github/my/rase-db-spneumoniae-sparc/isolates/001334.fa -k31 > output.fa 
$ l output.fa 
-rw-r--r--  1 karel  staff   157K Nov  5 23:49 output.fa

I.e., the output file is too small (but it doesn't fail anymore).

Hm, at this point I can't determine where the error is just by looking at the code. Could I get access to the spneumoniae file you're trying? The only thing I know of that could possibly cause is that if there are several records, they're not treated as continuous strings but as delimited. But I believe this is the correct behavior.

[karel-brinda]

It’s from this repo: https://github.com/c2-d2/rase-db-spneumoniae-sparc

On Sun, Nov 6, 2022 at 9:19 AM Ondřej Sladký @.***> wrote:

I'm currently getting some unexpected results.

$ ./kmers -p ~/github/my/rase-db-spneumoniae-sparc/isolates/001334.fa -k31 > output.fa $ l output.fa -rw-r--r-- 1 karel staff 157K Nov 5 23:49 output.fa

I.e., the output file is too small (but it doesn't fail anymore).

Hm, at this point I can't determine where the error is just by looking at the code. Could I get access to the spneumoniae file you're trying? The only thing I know of that could possibly cause is that if there are several records, they're not treated as continuous strings but as delimited. But I believe this is the correct behavior.

— Reply to this email directly, view it on GitHub https://github.com/GordonHoklinder/k-mers/pull/8#issuecomment-1304744944, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACC7KJRRFLFMQGAJSVEVKQ3WG5SY5ANCNFSM6AAAAAARYA626I . You are receiving this because your review was requested.Message ID: @.***>

-- Sent from my phone

[GordonHoklinder]

It’s from this repo: https://github.com/c2-d2/rase-db-spneumoniae-sparc On Sun, Nov 6, 2022 at 9:19 AM Ondřej Sladký @.> wrote: I'm currently getting some unexpected results. $ ./kmers -p ~/github/my/rase-db-spneumoniae-sparc/isolates/001334.fa -k31 > output.fa $ l output.fa -rw-r--r-- 1 karel staff 157K Nov 5 23:49 output.fa I.e., the output file is too small (but it doesn't fail anymore). Hm, at this point I can't determine where the error is just by looking at the code. Could I get access to the spneumoniae file you're trying? The only thing I know of that could possibly cause is that if there are several records, they're not treated as continuous strings but as delimited. But I believe this is the correct behavior. — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACC7KJRRFLFMQGAJSVEVKQ3WG5SY5ANCNFSM6AAAAAARYA626I . You are receiving this because your review was requested.Message ID: @.> -- Sent from my phone

Thank you!

[GordonHoklinder]

As the original issue has been solved, I'll merge this branch and deal with the other issue in #12 .