Unlike in the early days of breseq, installation of samtools/htslib can now be done by typical user through package managers. It makes sense to remove this code from the breseq codebase so that it can more easily benefit from bugfixes and continued development of those tools (e.g., CRAM files).
This change will require checking compatibility with different samtools/htslib versions and then being sure to update packages on Bioonda, homebrew, etc.