2.0.0

• Added --custom-reference-fasta and --custom-reference-genome options for mity call, mity normalise and mity runall
• Updated and added new mitomap sources (see mity_report_documentation for more detailed updates). Note that these changes are breaking and affect the behaviour of mity report.
• Added new option for mity report to additionally output the annotated vcf file as a xlsx file: --output-annotated-vcf.
• Fixed mity report output file name from prefix.annotated_variants.xlsx -> prefix.mity.report.xlsx.
• Added and improved documentation including: change_log, custom_report_configs, mity_report_documentation, future_improvements.
• Added ruff.toml for formatting.
• Removed custom calculations for ALLELE FREQUENCY MITOMAP which was derived from old mitomap Genbank Frequency. This is replaced with the new Genbank Frequency numbers from updated mitomap. See mitomap sources for more details.
• Fixed but in mity report when the sheet name is longer that 31 characters.

1.2.0

• Added --custom-reference-fasta and --custom-reference-genome options for mity call, mity normalise and mity runall
• Added new option for mity report to additionally output the annotated vcf file as a xlsx file.
• Added and improved documentation including: change_log, custom_report_configs, mity_report_documentation, future_improvements.
• Fixed but in mity report when the sheet name is longer that 31 characters.

1.1.0

• Fixed an issue where the report-config.yaml and vcfanno-config.toml files where not being found by mity.
• Added options to specify custom report and vcfanno config files.
• Added --contig as an option to mity report to specify the contig.
• Added annotations for MT and chrM. mity will default to using MT if the --contig option is not provided.
• Added vcfanno as a dependency to the Dockerfile.
• Added a runall option to run mity call, mity normalise, and mity report sequentially. This option supports all options from call and report.

1.0.0

• Refactored all modules of mity to support newer versions of python and other dependencies.
• Updated mity to use pysam for all vcf / bam / cram file manipulation
• Updated mity report to use vcfanno for annotating variants.
• Updated mity merge to use pysam concat and pysam isec for merging the files.
• General performance enhancements across all mity modules

0.4.0

Includes x38 support, CRAM, mitomap scores and pathogenic variant annotations from MitoTip

What's Changed

Full Changelog: 0.3.1...0.4.0

0.1.0

major documentation update