Version 1.10.0

Important Notes:

• Beginning with Version 1.8.0, the macOS binary provided by the BISCUIT maintainers will be built for the Apple M-series (arm64) CPU. For those with macOS using an Intel (x64_64) CPU, BISCUIT is available through bioconda or can be built from source.
• Beginning with Version 1.4.0, BISCUIT no longer needs submodules. Therefore, the GitHub-generated Source code (zip) and Source code (tar.gz) links may contain all necessary files. If preferred, release-source.zip is guaranteed to contain all BISCUIT source files.
• Beginning with Version 1.0.0, BISCUIT is no longer backwards compatible with Version 0.3.16 and earlier.

Date Created:

• 24 July 2026

General Changes:

• Updates to testing framework.

Changes affecting specific subcommands/scripts:

• align:
  • TLEN entry (SAM column 9) now properly adheres to SAM specification. Before, TLEN was calculated as (rightmost location) - (leftmost location) regardless of the orientation of the reads and would result in a TLEN that was always positive. Now, the magnitude remains the same as before, but the correct sign is given (rightmost segment is -, leftmost is +).
  • Seeds that span an asymmetric scoring violation (e.g., T → C) will now be trimmed to the longest violation-free subinterval, rather than be discarded. See commit e378206 for more details.
• postalt:
  • New subcommand
  • Processes an aligned SAM/BAM to prefer primary chromosomes over unplaced/alt contigs.

Bug Fixes:

• Issue #76 point 3 addressed. (Further unexplained mismappings). Reported by lh3.
• Issue #76 point 4 fixed. (Improper TLEN sign). Reported by lh3.