count_ss_match uses wrong file

[johnlamb]

Hi
See

CONFOLD/confold.pl

Line 1459 in 6b29b50

sub count_ss_match{

In the count_ss_match function, $file_sec is sent in as a parameter(in both instances when the function is used it is the secondary structure file that is sent in). However, this file is never referenced and %residue_ss1 is instead created from $file_fasta.
This causes the later comparison to compare amino acid vs secondary structure characters which will only work in cases of H, E and C and will hence give a wrong secondary structure match count.
I am happy to do a pull request with a correction if you can confirm it is a bug.

[badriadhikari]

Yes, I confirm that this is a bug and it should be fixed. This is extremely trivial though. The comparison results are only used for visualization/logging purposes and do not impact any model generation and selection.

[jianlin-cheng]

Would you like for the user to fix it or to fix it by yourself? You can reply to the user with your plan. Thanks. Jianlin

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On Tue, Feb 12, 2019 at 8:36 AM Badri Adhikari ***@***.***> wrote: Yes, I see that this is a bug and should be fixed. This is extremely trivial though. The comparison results are only used for visualization/logging purposes and do not impact any model generation and selection. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ATiD8dtglKuSHhhJB5sRcM6VRqK3YpBcks5vMtFogaJpZM4a1w6Y> .

[badriadhikari]

This is taken care!

[jianlin-cheng]

Great. Thanks! --Jianlin

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On Tue, Feb 12, 2019 at 2:29 PM Badri Adhikari ***@***.***> wrote: This is taken care! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ATiD8fZh-pADjVDhEqf2l6y0NsSPs0cXks5vMyQlgaJpZM4a1w6Y> .