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Ran 19 Nov 2025 05:21PM UTC

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Committed 19 Nov 2025 05:07PM UTC coverage: 97.007% (+0.04%) from 96.97%

Job # 19509852411.3

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push

github

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web-flow

Commit Message

Fixes for #172 (#175)

* Avoid calling permutedims when reading an MSA

* Refactor _fill_aln_seq_ann! to use IOBuffer

* Use write instead of print

* Enhance filtering functions in Annotations and GeneralParserMethods for better handling of AbstractStrings and improved performance

* Refactor _filter function to accept AbstractArray{Int} and improve performance in MSA annotations

* Add tests for MSA._filter and MSA._filter_mapping with empty and unicode inputs

* Optimize _filter (boolean mask) function avoiding the small zip penalty

* Test: always Int mask

* Test: Force int_mask only for _filter

* Test: Use blocks (ranges) for filtercolumns!

* Test: UnitRange Take II

* Revert to best-performing version (f66ab6)

* Refactor: Improve column filtering logic to retain non-gap columns in MSA

* Fix: Update _columns_to_keep function to accept AbstractMatrix for better flexibility

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