Skip to content

Update remove_uninformative_sites_from_aln.pl #21

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
TT1972 wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Update remove_uninformative_sites_from_aln.pl #21

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
4 changes: 2 additions & 2 deletions remove_uninformative_sites_from_aln.pl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ sub main{
}

# Start checking if the site is informative or not
next if($removeAmbiguities && $refNt eq 'N'); # if it's informative, but the ref base isn't good, then skip
next if($removeAmbiguities && $refNt =~ /[NRYKMSWBHDV]/); # if it's informative, but the ref base isn't good, then skip
next if($removeGaps && $refNt eq '-'); # if it's informative, but the ref base isn't good, then skip

# See if the rest of this column shows that it is informative.
Expand All @@ -74,7 +74,7 @@ sub main{
}

# Check to make sure it doesn't have an N anywhere
next POSITION if($removeAmbiguities && $nt eq 'N');
next POSITION if($removeAmbiguities && $nt =~ /[NRYKMSWBHDV]/);
# Check to make sure there is no gap at all
next POSITION if($removeGaps && $nt eq '-');
}
Expand Down