VEuPathDB / VEuPathDB/repeat-masker-nextflow
Clarification on "Satellite" vs. "acro/centr" in RepeatMasker .summary
Open
Nobody has claimed this yet.
- Dominant language
- Perl
- Stars
- 1
- Forks
- 2
- PR merge metrics
- No merged PRs in 30d
Description
Hi,
I noticed something confusing in the .summary output of RepeatMasker.
In some samples I see:
Satellite -- -- --
acro 3 226 0.00%
centr 1 49 0.00%
While in other samples:
Satellite 3 306 0.00%
acro 3 226 0.00%
centr 1 49 0.00%
My questions are:
- What does it mean when the parent
Satelliteline shows--vs. when it shows a number? - Are
acroandcentralways considered subcategories ofSatellite? - For total calculation, should we treat the numeric value in
Satelliteas "unclassified satellites" and add it toacro+centr(when present)? - I also noticed that in the "Total" line at the
.summary, the values forSatellite,acro, andcentrare all added separately — i.e. they are not merged under oneSatellitetotal but contribute independently to the final sum. Is this the intended behavior?
Thanks!
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Review RepeatMasker’s .summary output and the Satellite, acro, and centr examples provided in the issue. Determine how parent and subcategory values are defined and included in the Total line, then document the answers and expected calculation behavior.
Written by the indexing model from the issue text.
Assessment
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100