segul -

- Rust
Published by github-actions[bot] almost 2 years ago

segul -

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.

- Rust
Published by github-actions[bot] almost 2 years ago

segul -

- Rust
Published by github-actions[bot] almost 2 years ago

segul -

- Rust
Published by github-actions[bot] about 2 years ago

segul -

- Rust
Published by github-actions[bot] about 2 years ago

segul -

- Rust
Published by github-actions[bot] about 2 years ago

segul - 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 header now use snake_case and more consistent across all features that output CSV.

- Rust
Published by github-actions[bot] over 2 years ago

segul -

- Rust
Published by github-actions[bot] over 2 years ago

segul -

- Rust
Published by github-actions[bot] over 2 years ago

segul -

- Rust
Published by github-actions[bot] over 2 years ago

segul -

- Rust
Published by github-actions[bot] almost 3 years ago

segul -

- Rust
Published by github-actions[bot] almost 3 years ago

segul - 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.

- Rust
Published by github-actions[bot] almost 3 years ago

segul -

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

- Rust
Published by github-actions[bot] over 3 years ago

segul -

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.

- Rust
Published by hhandika almost 4 years ago

segul -

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.

- Rust
Published by hhandika almost 4 years ago

segul - 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.

- Rust
Published by hhandika about 4 years ago

segul - v0.16.2

Fix version number errors.

- Rust
Published by hhandika about 4 years ago

segul - v0.16.1

Fix conflicting short commands.

- Rust
Published by hhandika about 4 years ago

segul - 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

- Rust
Published by hhandika about 4 years ago

segul - 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.

- Rust
Published by hhandika about 4 years ago

segul - 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.

- Rust
Published by hhandika about 4 years ago

segul - v0.13.1

• Fix issues including empty sequences in splitted alignments.
• Fix unmatched nchar counts in nexus and phylip output when splitting alignments.

- Rust
Published by hhandika about 4 years ago

segul - v0.13.0

• Fix errors in the nexus output datatype for amino acid sequence.
• Add a feature to split alignment given partition information.

- Rust
Published by hhandika about 4 years ago

segul - v0.12.0

• Add taxon summary to the summary stats feature.
• Summary stats now write the csv ouput 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.

- Rust
Published by hhandika over 4 years ago

segul - 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.

- Rust
Published by hhandika over 4 years ago

segul - v0.11.1

• Fix file count formatting for sequence extraction terminal output.
• Fix outdated error messages.

- Rust
Published by hhandika over 4 years ago

segul - 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.

- Rust
Published by hhandika over 4 years ago

segul - v0.10.1

• Fix terminal output for dry-run.
• Fix spinner messages.

- Rust
Published by hhandika over 4 years ago

segul -

Now can batch rename sequence IDs

- Rust
Published by hhandika over 4 years ago

segul -

Fix missing file extension issues when converting multiple sequences

- Rust
Published by hhandika over 4 years ago

segul -

Add a DNA to Amino Acic translation feature.

- Rust
Published by hhandika over 4 years ago

segul -

Fix inconsistent DNA character ordering when using a single input for summary statistics.

- Rust
Published by hhandika over 4 years ago

segul -

Fix missing wildcard options for id and filter subcommands

- Rust
Published by hhandika over 4 years ago

segul - v0.8.4

Fix errors in displaying proportion of parsimony informative sites for a single file input

- Rust
Published by hhandika over 4 years ago

segul -

• Minor performance improvement for sequence extraction.
• Bug fixes.

- Rust
Published by hhandika over 4 years ago

segul -

• Fix wrong help messages in the extract command arguments.
• Shows output directory in the terminal after extracting sequences.

- Rust
Published by hhandika almost 5 years ago

segul -

Fix issues missing summary subcommands

- Rust
Published by hhandika almost 5 years ago

segul -

A new feature to extract sequences based on user-defined IDs. The new feature comes with regular expression support.

- Rust
Published by hhandika almost 5 years ago

segul -

Fix unmatched version numbers.

- Rust
Published by hhandika almost 5 years ago

segul -

• Add spinner for converting a single file.
• Output names for concatenating filtered sequences is now default to the directory name with parameters as sufixes.
• 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.

- Rust
Published by hhandika almost 5 years ago

segul -

Try to fix Windows CI issues.

- Rust
Published by hhandika almost 5 years ago

segul -

Try to fix Windows CI issues.

- Rust
Published by hhandika almost 5 years ago

segul - v0.6.4

Add Apple M1 support

- Rust
Published by hhandika almost 5 years ago

segul - v0.6.3

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.6.2

- Rust
Published by hhandika almost 5 years ago

segul - v0.6.1

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.6.0

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.5.0

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.4.0

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.3.16

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.3.15

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.3.14

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.3.12

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.3.11

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.3.10

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.3.9

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.3.8

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.3.7

- Rust
Published by github-actions[bot] almost 5 years ago

segul - v0.3.6

- Rust
Published by github-actions[bot] almost 5 years ago

segul -

- Rust
Published by hhandika almost 5 years ago

segul -

- Rust
Published by hhandika almost 5 years ago

segul -

- Rust
Published by hhandika almost 5 years ago

segul -

- Rust
Published by hhandika almost 5 years ago

segul -

- Rust
Published by hhandika almost 5 years ago

segul -

- Rust
Published by hhandika almost 5 years ago