Skip to content

Fix for occasional seg fault #50

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ryanbarouki wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Fix for occasional seg fault #50

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 9 additions & 1 deletion lib/src/msa_op.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -348,13 +348,21 @@ int convert_msa_to_internal(struct msa* msa, int type)

t = a->to_internal;
msa->L = a->L;
int unknown = 0;
if (t[(int)'X'] != -1) {
unknown = t[(int)'X'];
} else if (t[(int)'N'] != -1) {
unknown = t[(int)'N'];
}

for(i = 0; i < msa->numseq;i++){
seq = msa->sequences[i];
for(j =0 ; j < seq->len;j++){
if(t[(int) seq->seq[j]] == -1){
WARNING_MSG("there should be no character not matching the alphabet");
WARNING_MSG("offending character: >>>%c<<<", seq->seq[j]);
WARNING_MSG("offending character: >>>%c<<<, replacing internal alphabet value: %d with unknown: %d", seq->seq[j], seq->s[j], unknown);
/* exit(0); */
seq->s[j] = unknown;
}else{
seq->s[j] = t[(int) seq->seq[j]];
}
Expand Down