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Handle features of origin of plasmid - #11

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BradyAJohnston merged 9 commits into
mainfrom
10-split-origin
Sep 2, 2025
Merged

Handle features of origin of plasmid#11
BradyAJohnston merged 9 commits into
mainfrom
10-split-origin

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@BradyAJohnston

@BradyAJohnston BradyAJohnston commented Sep 28, 2023

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Fixes #10

Summary

Properly handles plasmid features that span across the origin. Features like join(4891..5096,1..751) are now correctly processed as continuous features instead of being truncated.

Changes

  • Fixed origin-spanning feature parsing: Updated coordinate system offset logic in R/dataframe.R
  • Added comprehensive tests: New test cases for edge cases and real-world validation
  • Updated GitHub Actions: Upgraded to latest versions (actions/checkout@v4, streamlined matrix)
  • Fixed configuration issues: Syntax error in _pkgdown.yml, URL consistency in DESCRIPTION
  • Added documentation: Proper roxygen2 docs for stat_arrow() function

Verification

The TurboID gene from the example file now correctly shows as 957bp (instead of truncated) with proper continuous coordinates after offset transformation.

🤖 Generated with Claude Code

@BradyAJohnston
BradyAJohnston merged commit 2d3930d into main Sep 2, 2025
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@BradyAJohnston
BradyAJohnston deleted the 10-split-origin branch September 2, 2025 19:59
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read_gb loses part of plasmid feature that spans across the start site

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