Version 1.5.0

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:

• 6 May 2024

General changes:

• Add citation to README.

Changes affecting specific subcommands/scripts:

• Added extended CIGAR operations (= and X) for pileup and epiread.
• epiread:
  • Added ability to work with modification SAM tags (MM/ML) with the -M flag and the -y FLOAT option, which adjusts the minimum probability that a modification is correct.
  • Updated the -L option from using hard coded read lengths to now accept an integer input (-L INT) specifying the maximum read length.
  • Added error messages when reads longer than the specified max length are found.

Bug Fixes:

• Issue #49 and #51 fixed (biscuit epiread wouldn't accept gzipped or bgzipped SNP BED files). Reported by njspix and fei0810.
• Issue #50 fixed (NM tag was being incorrectly set for C>T conversions on OB/CTOB reads). Reported by njspix.
• Add warning message and skip processing read when a negative start position is found when creating epiBED files.