v0.11.1

What's Changed

Added

• Python 3.13 added to GitHub Actions CI test matrix.
• Snakemake workflow section added to README.

Fixed

• multi_wps no longer crashes with ValueError: negative dimensions are not allowed when BED intervals produce degenerate windows (e.g. when expanded
  intervals exceed chromosome boundaries or when closely spaced TSS sites
  trigger overlap-trimming that inverts start/stop).
  • stop is now clamped to chromosome size when computing expanded windows.
  • Degenerate intervals (stop <= start) produced by overlap-trimming are
    silently skipped instead of being forwarded to worker processes.
  • wps now checks for stop <= start at function entry, emits a
    UserWarning, and returns an empty result rather than crashing.

Changed

• low_quality_read_pairs in utils now also checks the MQ (mate mapping
  quality) BAM tag and marks a read pair as low quality if the mate's mapping
  quality falls below min_mapq.

New Contributors

• @jojo0226 made their first contribution in #165

Full Changelog: v0.11.0...v0.11.1