Changelog¶

All notable changes to this project will be documented in this file.

For the full changelog, see CHANGES.md in the repository root.

[Unreleased]¶

476 automated tests covering all library modules and 32 of 33 CLI scripts
Type hints on all 33 CLI scripts and all library modules
11 bug fixes with regression tests
7 dead library modules removed (annoGene, fasta, orf, quantile, wiggle, cigar, changePoint)
Dead code classes removed: ParseSAM, QCSAM, CompareBED, 6 unused ParseBAM methods
Performance: numpy vectorization in bamTowig(), readsNVC(), single-pass CIGAR loops
All 33 CLI scripts migrated from optparse to argparse
pandas removed as direct dependency
Shared cli_common.py module consolidates utilities from 14+ scripts
Python 3.13 compatibility fixes

Initial modernized release.