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@KondratievaOlesya KondratievaOlesya released this 05 Dec 13:54
· 20 commits to main since this release
0.2.2
d2ce376
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Learn about vigilant mode.
  • Change apply_variant_to_repeat function for applying VCF variants to STR panel sequences.
    • Locally normalizes variants (pos, ref, alt) by trimming shared prefix/suffix before applying.
    • Applies the full ALT if the normalized variant starts inside the STR; only clips when the variant starts before the STR and overlaps it.
    • Handles REF/ALT in a case-insensitive way and matches the output case to the STR panel sequence.
    • Includes unit tests for:
      • variants overlapping STR boundaries,
      • long homopolymer variants extending beyond the STR,
      • lowercase REF/ALT vs uppercase/lowercase STR panel.
  • Filter records with same alt and ref (happens if mutation is not normalized and actually happens outside of STR region)
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