v1.6.4

• Patch to fix Pangolin version updating when starting with a current local installation of pangolin v3.1.11 or below where the --all-versions flag did not exist. This prevents such error from exiting the entire pipeline and allowing for the software to be updated
• Modified output when software versions do not match when assessing lineage output as opposed to exiting the program with an error outright
• Added Breseq parameters for minor variant thresholds to be defined by the user
• Defaults are set automatically for added Breseq parameters (see below), if not found in existing (i.e., previous versions of) config.yaml files

Updates to config.yaml:

# Used as --polymorphism-minimum-variant-coverage-each-strand, --polymorphism-frequency-cutoff arguments
# Parameters needed to determine thresholds for minor variant detection
polymorphism_variant_coverage: 2
polymorphism_frequency: 0.05