Pre submission updates#118

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OberonDixon merged 18 commits intomainfrom

Nov 25, 2025

Commits on Nov 11, 2025

Commits on Nov 12, 2025

Add relative=False option (absolute coordinates) for enrichment profiles
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Add support for pseudouridine by supporting mod codes more than one character long
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Commits on Nov 13, 2025

Improve plot_read_browser customizability
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Commits on Nov 14, 2025

Read length management adjusted for gapped alignments e.g. RNA with splicing. TODO: adjust logic once we get true read start and end in modkit
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Add span_full_window parameter to select only reads that both are within and cover the entirety of the window used for loading
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Move metadata per-read parsing to below the read saving functionality. The previous order introduced a bug and failed tests because of strand mismatch. This now passes all tests while maintaining t…
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Commits on Nov 15, 2025

Commits on Nov 19, 2025

ruff format
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