All notable changes to this project will be documented in this file. The project loosely follows semantic versioning. The following subheaders are used in the change log:
- Added for new features.
- Changed for changes in existing functionality.
- Deprecated for once-stable features removed in upcoming releases.
- Removed for deprecated features removed in this release.
- Fixed for any bug fixes.
- Security to invite users to upgrade in case of vulnerabilities.
The topmost subheader is always [wip], and lists what is currently being worked on. Below the work in progress, a subheader for each notable release lists the main changes introduced by that release.
- Peptide sequence is now included in --write-discriminative-peptides output
- --reassign-taxids now allows to modify taxid assignments for refseqs in the taxref DB.
- --peptide-fasta to include peptide sequences in taxonomic composition output file.
- --add-annotations to add annotations to annotation DB.
- New helper script: get_peptide_sequences.py to print discriminative peptides and their taxonomic assignments.
- Removed Terrabacteria group with no rank from output listing.
- No longer try to insert taxids into taxref DB when pre existing sample DB is used.
- Taxonomic composition estimation with xslx output.
- Antibiotic resistance detection.