gappa v0.5.1

Notable Changes

• Reduce memory footprint of Squash Clustering.

gappa v0.5.0

This is mostly a maintenance and quality-of-life update that improves usability and cleans up the interface.

Notable Changes

• Restructure analyze and examine modules.
• Move random data generation commands to own module.
• Add log file option.
• Improve error reporting and logging.
• Add tool commands, citation, license and version.
• Add proper formatting to help messages.
• Refine and add documentation of several commands.
• Several bug fixes.

gappa v0.4.0

Notable Changes

• Support for jplace standard versions 1 and 2.
• Add prepare random-placements command.
• Better support for Mac OS.
• Fix bioconda/bioconda-recipes#14765

gappa v0.3.0

IMPORTANT

Unfortunately, this release has a broken commit hash for the genesis version. It hence does not work when using CMake to download the genesis dependency. Instead, you have to use git clone --recursive or some other git command to pull the correct genesis version. You have to pull this commit.

We do not fix this release, so please download a more recent release instead if needed. Sorry for the inconvenience.

Notable Changes

• Add analyze placement-factorization command.
• Add edit multiplicity command.
• Add edit split command.
• Add prepare random-alignment command.
• Add prepare random-tree command.
• Add prepare taxonomy-tree command.

gappa v0.2.0

Changes:

• Add and change the output options for assign command (#5).
• Fix #6, where some large files were not parsed correctly.

gappa v0.1.0

Initial release that starts version counting. For now, the tool should not be considered stable. Anything may change at any time. More commands and features will be added. This release is mainly intended as a point of reference (see #4).