v0.3.0

[0.3.0] - 2026-01-12

• Mismatch handling between VCF and STR panel
  • Added support for cases where the VCF reference does not exactly match the STR panel.
    • ignore_mismatch_warnings (bool, optional)
      Suppresses warnings when the STR panel sequence does not match the VCF reference allele.
      Default: False.
    • mismatch_truth (str, optional)
      Defines which source is treated as correct when a mismatch is detected:
      • panel: trust the STR panel sequence (default).
      • vcf: trust the VCF reference sequence.
      • skip: skip loci with mismatches.

v0.2.2

• 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)

v.0.2.1

[0.2.1] - 2025-11-26

• Reformatted code for consistency and style.
• Added tox-based test matrix and GitHub Actions CI.
• Updated repeat unit counting logic to use the maximum length of uninterrupted motif runs, and added tests for complex cases.

[0.2.0] - 2025-11-25

• Fixed error in detection of unsorted VCF files
• Fixed bug that caused annotation to stop at chromosome 9; annotation now runs through all chromosomes

v0.1.0

Release project on PyPi.

• Core functionality:

  • STR annotation for VCF files using BED reference
  • Support for indels and SNVs in repeat regions
  • Calculation of repeat copy numbers (REPCN)
  • Perfect repeat detection
  • Reconstruction of full repeat sequences

• Parser system:

  • BaseVCFParser abstract interface for extensibility
  • GenericParser implementation supporting standard VCF fields (GT, AD, DP)
  • Easy to extend with custom parsers

• API (Library usage):

  • STRAnnotator class for programmatic access
  • annotate_vcf() convenience function
  • Support for both single file and batch directory processing

• CLI (Command-line usage):

  • strvcf-annotator command-line tool
  • Single file mode: --input and --output
  • Batch directory mode: --input-dir and --output-dir