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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,
The text was updated successfully, but these errors were encountered:
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 inhmmalign
(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,
The text was updated successfully, but these errors were encountered: