Skip to content
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.

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

allcol option has gone. #8

Open
lguangyu opened this issue Oct 22, 2019 · 1 comment
Open

allcol option has gone. #8

lguangyu opened this issue Oct 22, 2019 · 1 comment

Comments

@lguangyu
Copy link

Hi All,

I'm recently trying out building a custom reference geneset for Xander. I noticed the preparing script is a bit picky on the hmm suite version. After some struggling, I learned that the --allcol option in hmmalign (called by that script) has been long gone since 3.0 - the version which the manual asks for, for more than 9 years. The patch is also not compatible with 3.1 or later versions (line offset in 3.1 and content change in 3.2). I then assume the preparing pipeline calls for exactly some pre-release version of 3.0. but the Xander pipeline script calls for 3.1b1 (the version tested by developer, appearently). This inconsistency is confusing.
Currently I have to manually patch hmm 3.1 or 3.2 (latest) and adopt the prepare script to get rid of allcol calls. But it appears to be too many changes for a release, while I have no idea how much these changes would affect the results and accuracy. Does anyone have more suggestion on building a custom database?

Best,

@asl
Copy link

asl commented Feb 12, 2020

@lguangyu Sorry for somehow advertising post, but you can give Pathracer (http://cab.spbu.ru/software/pathracer/) a try

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants