Version 1.4.0

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.

Important Note: This version is not backwards compatible with BISCUIT Version 0.3.16 and earlier.

Date Created:

• 8 January 2024

General changes:

• Moved to CMake-based build system
  • CMake (min. version 3.21) must be installed to build BISCUIT
  • See documentation for more details about building with CMake
• Removed submodule dependencies
  • Libraries that previously were submodules are now downloaded and built via CMake build process
  • --recursive option no longer necessary for cloning BISCUIT
• klib has been removed as a full dependency
  • Specific klib utilities necessary for build are available either in lib/aln or htslib
• Updated to htslib version 1.18
• Release process has now been partially automated

New subcommand:

• help: Same as just running biscuit, but allows for a clear entry point to BISCUIT's usage

Changes affecting specific subcommands/scripts:

• bc:
  • Cell barcode and artificial UMI now output to read name (name_barcode_umi) for UMI-tools compatibility
  • Cell barcode no longer output to read comment
• align:
  • memchain.c B-Tree traversal method updated
  • -9 option extracts both cell barcode and UMI from read name (previously only the cell barcode from the read comment) for UMI-tools compatibility
• pileup: (and others)
  • Decoupled pileup source code from other subcommands

Bug Fixes:

• Fixed memory leak in biscuit epiread
• Corrected version info in biscuit version
• Check if output SAM file can be written to in biscuit bsconv
• Typo in --keep-tmp-files option of QC.sh. Fixed by kew24 (PR #46).