Version 1.1.0

Source code (zip) and Source code (tar.gz) are generated by GitHub and may not contain all required submodules. Use these at your own risk! It is suggested to use the release-source.zip if downloading the source code.

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

Date Created:

• 7 July 2022

General changes:

• Copyright years updated.
• Implicit fallthrough warnings fixed for more recent versions of GCC.
• Makefile has no explicit calls to gcc. All calls happen through $CC.

Changes affecting specific subcommands/scripts:

• epiread:
  • Gzipped BED files are now able to be used as inputs to -B.
  • Empty reads (those with only F, x, and/or P in them) are removed by default. If included, the -E option will leave these reads in the output file.
  • Add long read functionality (-L option).
  • Add "-" in old epiread format for C's that are filtered to maintain alignment with C's occurring in the reference.
• asm:
  • Fisher's exact and chi-squared p-values are now output in scientific notation, rather than as decimals.

Bug Fixes:

• Issue #19 fixed (memory leak in -p option of biscuit align).
• Issue #21 fixed (implicit reliance on alphabetical ordering of SQ tags in BAM).
• Issue #22 fixed (incorrect NOMe output in pileup).
• Fix reading Bismark BS strand flags from BAM.