VEuPathDB / VEuPathDB/repeat-masker-nextflow

Clarification on "Satellite" vs. "acro/centr" in RepeatMasker .summary

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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:

  1. What does it mean when the parent Satellite line shows -- vs. when it shows a number?
  2. Are acro and centr always considered subcategories of Satellite?
  3. For total calculation, should we treat the numeric value in Satellite as "unclassified satellites" and add it to acro + centr (when present)?
  4. I also noticed that in the "Total" line at the .summary, the values for Satellite, acro, and centr are all added separately — i.e. they are not merged under one Satellite total but contribute independently to the final sum. Is this the intended behavior?

Thanks!

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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

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