mmmvi-v0.10.2

• Better handling of cases where an empty directory has been provided to --mutations
• Add --input as a synonym of --bam
• Fix bug that can crash the program during the calculation of the theoretical maximum number of mutations per read

mmmvi-v0.10.0

• Now able to read variant definitions directly from Public Health England's Standardised Variant Definitions
  • In place of the mutations file, you may provide a directory containing PHE-formatted YAML files
  • The tabular mutations file is still valid
• On a failed parse of the tabular mutations file, mmmvi will report the mutation string which caused the failure
• If you have used mmmvi in your work, you can now use the --cite flag to generate a BibTeX citation

mmmvi-v0.9.0

• Significantly shortens the time required to analyze a sample (~ 3.5 hours -> 1 hour in testing)
• Slightly reduces memory requirements (14 GB -> 12 GB)
• Fixes a bug which produced faulty overlap counts in some cases
• Enforce numerical ordering of columns in summary.txt

mmmvi-v0.8.2

• Fixes a bug which dramatically slowed generating the read species report
• Non-user facing code reorganization

mmmvi-v0.8.1

• Fixes a bug where mutations in the read species report would be repeated for each variant that included that mutation
• Add logging events for beginning and completing the program
• Documentation improvements

mmmvi-v0.8.0

• Enhanced summary output
  • Adds theoretical maximum number of mutations per read based on distances between mutations and median read length
  • Adds coverage of mutations to see how many of the signature mutations are represented in the sample

mmmvi-v0.7.0

• Fix regression which failed to count read species which spanned multiple variants
• Add basic run time logging

mmmvi-v0.6.3

• Make positions and mutations reporting consistently structured
• Fix bug which prevented overlapping reads from being counted for deletion mutations

mmmvi-v0.6.2

• Fix bug which counted read species multiple times if they appeared in multiple VOCs
• Improve documentation
• Merge and simplify logic for calling variants in both Nanopore and Illumina data

mmmvi-v0.6.0

• Now handles multiple alternative mutations at the same position in the same VOC

  • e.g. G23012A and G23012C

• Validates substitution lengths versus wildtype to catch malformed mutation strings earlier