# Release Notes ## v0.22.1 ### Bug Fixes - Sequence filtering now does not enforce input is an alignment. ## v0.22.0 ### New Features - Filter sequences based on gaps or sequence length. - Add a proportion of missing data parameter to the alignment filtering. ### API Breaking Changes - Rename classes and methods to improve clarity and consistency. - Remove unnecessary mutability for conversion modules. - Partition conversion moved to align module. - Output directory and output format arguments for extraction are now required in the new instance of the extraction struct. ## v0.21.3 - Try to fix ARM CI issues. ## v0.21.2 - Fix auto detect sequence format issue does not match the GUI input. ## v0.21.1 - Fix extra commas in the alignment summary CSV output. - Fix missing proportion of missing data in alignment summary. - Fix issues when inputting list of IDs for sequence extraction and removal. Now, require equal sign and semi-colon to separate the IDs. - Fix spacing and incorrect symbol issues in the terminal output. ### v0.21.0 - Alignment summary now is written to file. - Read summary with `complete` option now writes per read position results to compressed zip file. - Prefix option for read, contig summary, and ID extraction. - More consistent CSV header names for all summary statistics, and sequence ID map. ## v0.20.2 - Fix CI issues. ## v0.20.1 - Fix empty result when summarizing a single contig file. - Fix CI issues. ## v0.20.0 - ID parsing result is now in a directory consistent with other subcommands. ## v0.19.2 - Fix CI issues. ## v0.19.1 - Fix CI issue when building windows binary. ## v0.19.0 New features: - Directory input auto detect sequence format based on the file extension. - New summary statistics for raw reads and contigs. - 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. - Add integration tests. 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 name consistent with subcommand name for statistics function. ## v0.16.3 - Fix output option show up when it does not use by the partition subcommand. - Fix unclear error messages when failing to infer partition based on the file extension. ## v0.16.2 - Fix version number errors. ## v0.16.1 - Fix conflicting short commands. ## v0.16.0 - New feature to convert partition formats. - Now, can parse codon partition. - Check partition format in the sequence file when splitting alignments. - Fix incorrect data type in raxml partition when the input is amino acid sequences. - Clearer command help output (now use [clap](https://docs.rs/clap/latest/clap/) v3). ## v0.15.0 - Add an overwriting flag to all subcommands to allow overwriting existing output files or directories. - Fix typos in error messages. - Check sequences for duplicate IDs are the same. Let users know in the error messages. ## v0.14.0 - Add support for RaXML partition that does not contain datatype. - Add an option to prefix output filename when splitting alignments. - Replace dot with underscore in the partition locus name. - Print partition information when splitting alignments. ## v0.13.1 - Fix issues including empty sequences in split alignments. - Fix unmatched number of character counts in nexus and phylip output when splitting alignments. ## v0.13.0 - Fix errors in the nexus output datatype for amino acid sequence. - Add a feature to split alignment given partition information. ## v0.12.0 - Add taxon summary to the summary stats feature. - Summary stats now write the csv output files to a directory. - Allow to add prefix for summary stats csv output files. - Fix spaces issue in showing filtering parameters in the log output. ## v0.11.2 - Fix confusing input name in the terminal output. - Improve fasta parsing performance. - Fix issues when the app keeps processing when no alignments left after filtering. ## v0.11.1 - Fix file count formatting for sequence extraction terminal output. - Fix outdated error messages. ## v0.11.0 - Add feature to map sample distribution across a collection of alignments. - Dir and file exist prompts now show the file names. - Simplify input option. Wildcard option is now a part of input option. - Print output format. ## v0.10.1 - Fix spinner messages. - Fix dry-run terminal output. ## v0.10.0 - Add feature to batch renaming sequence IDs. ## v0.9.1 - Fix missing file extension issues when converting multiple sequences ## v0.9.0 - Add a DNA to Amino Acid translation feature. ## v0.8.6 - Fix inconsistent DNA character ordering when using a single input for summary statistics. ## v0.8.5 - Fix missing wildcard options for filter and id subcommands. ## v0.8.4 - Fix errors in displaying proportion of parsimony informative sites for a single file input. ## v0.8.3 - Minor performance improvement for sequence extraction. - Fix multiple newlines after spinners when using ID subcommands. ## v0.8.2 - Fix wrong help messages in the extract command arguments. - Shows output directory in the stdout after extracting sequences. ## v0.8.1 - Fix issues missing summary subcommands. ## v0.8.0 - Add new feature to extract sequence file based on user-defined IDs. ## v0.7.1 - Fix version unmatched version numbers. ## v0.7.0 - Add spinner for converting a single file. - Output names for concatenating filtered sequences is now default to the directory name with parameters as suffixes. - Allow "ignore" in the summary data types. - Fix issues on specifying a directory for summary stats. - Help info now shows the type of values required for the arguments. - Fix typos in panic messages. ## v0.6.6 - Try to fix Windows CI issues. ## v0.6.5 - Fix CI issues ## v0.6.4 - Update release rules. ## v0.6.3 - CI release changes. ## v0.6.2 - Clearer terminal messages. ## v0.6.1 - Fix CI token access. ## v0.6.0 - Add support for percent parsimony informative. ## v0.5.0 - Allow to specify both the directory and file name for concatenating alignments. - Clearer prompt messages. - More consistent letter cases and spacing for spinner. - Concat filtered alignment now default to nexus. No need to specify. ## v0.4.0 - Avoid overwriting existing files or directory. Now, ask user to remove or abort. - Concatenate results now in a directory. - Better error handling - Fix stack overflow when getting unique ids. ## v0.3.16 - Change panic implementation to C-style abort. - Fix issues with too many redundant error messages when panic occurs in multi-threading tasks. ## v0.3.15 - Print data type in the input information. ## v0.3.14 - Fix another CI issue. ## v0.3.13 - Update release steps. ## v0.3.12 - CI fix with newer container. ## v0.3.11 - Add support for older linux. ## v0.3.10 - Change CI implementation. ## v0.3.9 - Fix CI errors. ## v0.3.8 - More consistent error messages for the filter subcommand. ## v0.3.7 - Better error handling. ## v0.3.6 - Fix issues when concatenating filtered alignments. Now, enforce users to input required arguments. ## v0.3.5 - Change option "format" to "input-format" for consistency with "output-format". - Fix missing a new line after spinner message in converting sequences in a directory. ## v0.3.4 - Fix wildcard issues on windows. ## v0.3.3 - Fix issue with summary printing. ## v0.3.2 - Fix error prematurely writing a log file. ## v0.3.1 - Fix welcome screen showing up when checking the app version. ## v0.3.0 - Add new features: alignment filtering, id finding, and summary statistics. - More consistent terminal output. - Add sequence checking for fasta input. - Faster parser. - Improvement in memory allocation. ## v0.2.0 - Add support for interleaved outputs. ## v0.1.1 - Faster fasta concat. ## v0.1.0 - First release.