v0.21.0

1. Instead of in the log file, alignment summary is now in a separate output file with alignment-summary suffix.
2. Read summary with complete option now writes per read position results to compressed zip file.
3. Prefix option for read, contig summary, and ID extraction.
4. CSV headers now use snake_case and more consistent across all features that output CSV.

v0.20.2

Fix missing build commands.

v0.20.1

Fix musl errors ci.

v0.20.0

ID parsing result is now in a directory consistent with other subcommands.

v0.19.2

Bump version number.

v0.19.1

Fix CI issues for building windows binary.

v0.19.0

New features:

• New summary statistics for raw reads and contiguous sequences.
• Auto detect input format when using directory input
• New command line structure.

Bug fixes:

• Fix translation table errors.
• Update deprecated dependencies.
• Fix extract output issues.

v0.18.1

• Fix colored terminal dependency deprecation issues.
• Fix inconsistent header alignment when printing summary statistics to the terminal.

v0.18.0

New features:

• Add an option to generate sequence statistics for each locus.
• More taxon statistics: proportion of missing data, nucleotide counts, GC content and AT content.
• Add message when choosing "no" folder exists.

Bug Fixes:

• Fix compiling issues.
• Fix command conflicts when using the option remove-re-all.

v0.17.0

New Features:

• Add a feature to remove sequence based on user-defined IDs.
• Add regular expression support to rename sequence IDs.
• Add string replacement option to rename sequence IDs.
• Add option to filter based on the present of all user-defined taxa.
• Replace site counts with character counts in the taxon summary.

Bug Fixes:

• Fix error messages when finding empty matrix.
• Fix missing character counts in amino acid alignment summary.
• Fix input and output format character cases.
• Fix conflict with percent when filtering alignments.
• Fix command conflict errors.
• Make output directory names consistent with sub-command names.