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Locus matching: tagged loci, composite rows, exact preference - #23

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locus-review-fixes
Oct 2, 2026
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YPARK merged 1 commit into
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locus-review-fixes

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@YPARK YPARK commented Oct 2, 2026

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Review follow-ups to the strict colon rule (these were meant for 0.7.1 but missed its merge).

  • The gene rule strips a feature-type tag from a coordinate and keeps the rest whole: chr1:0-100_Peaks matches chr1:0-100 again; Mixed keys it as 1:0-100.
  • GeneIndex finds a row's locus part (whole name, /-core, or the locus of an id_name join such as chr1:100-200_GENE1). A locus query matches the same name first, then locus key plus rest, then a bare key; a whole-locus row wins its key over one that only starts with it.
  • h5ad feature types are read from var/feature_type or var/feature_types (scanpy, muon), so mixed files get their peaks converted.
  • The non-colon warning fires at a tenth of the axis, and also when an explicit overlap kind finds no colon loci. An untyped list that only partly reads as intervals is logged, and the import count is rows.

Requires legume-genomic-types 0.5.3. Version 0.7.2.

- The gene rule strips a feature-type tag from a coordinate and keeps
  the rest whole: chr1:0-100_Peaks matches chr1:0-100 again; Mixed keys
  it as 1:0-100.
- GeneIndex finds a row's locus part (whole name, '/'-core, or the
  locus of an id_name join such as chr1:100-200_GENE1). A locus query
  matches the same name first, then locus key plus rest, then a bare
  key; a whole-locus row wins its key over one that only starts with it.
- h5ad feature types are read from var/feature_type or
  var/feature_types (scanpy, muon).
- The non-colon warning fires at a tenth of the axis, and also when an
  explicit overlap kind finds no colon loci; an untyped list that only
  partly reads as intervals is logged; the import count is rows.

Requires legume-genomic-types 0.5.3. Release 0.7.2.
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YPARK merged commit 636d950 into main Oct 2, 2026
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YPARK deleted the locus-review-fixes branch October 2, 2026 01:20
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