Releases | Open Source Science

BTE - Haplotype Bugfix

Contains a bugfix leading to incorrect haplotype prediction due to a mishandled copy.

Scientific Software - Peer-reviewed - Cython
Published by jmcbroome 9 months ago

BTE - Re-Release to Trigger Archival

After integration with Zenodo's automated archival service, a new release is required to trigger the initial synchronization.

Scientific Software - Peer-reviewed - Cython
Published by jmcbroome almost 3 years ago

BTE - New Features and Function Renaming

This release includes a few minor changes:

The function writenewick now writes to a file. The original functionality is available as getnewick.
Added a new function to set the branch length of an already defined node to an arbitrary value.
Added a new function to get the last common ancestor (LCA) of 2+ node IDs.

Scientific Software - Peer-reviewed - Cython
Published by jmcbroome almost 3 years ago

BTE - Improved Annotations and Mutation Information

This release includes improved functionality around annotations and mutation information.

Annotations can now be get/set in a nodeid:[ann1,ann2] format compatible with internal data structures with dumpnodeannotations() and applynodeannotations(). A dictionary in ann:nodeid format can be created with getannotations(). This addresses https://github.com/jmcbroome/BTE/issues/15. Deprecated functions dumpannotations() and apply_annotations() are replaced.
The user can now get a dictionary with mutational attribute information for each mutation of a node with getmutationinformation(). This includes otherwise inaccessible data, such as chromosome and the reference nucleotide of the position.

Additionally, this release fixes bugs, updates the documentation site, and expands the testing suite.

Scientific Software - Peer-reviewed - Cython
Published by jmcbroome about 3 years ago

BTE - Versioning and bugfixes

Minor tweaks to behavior, handling rare bugs, and change to boost-cpp version in an attempt to make BTE coinstallable with UShER.

Scientific Software - Peer-reviewed - Cython
Published by jmcbroome about 3 years ago

BTE - Bugfixes

This patch addresses the following issues:

Fix JSON writing so that subtrees are correctly extracted instead of writing a global JSON regardless of sample input.
Fix the AAChange class so that the repr does not attempt to access a deprecated attribute (preventing AAChange objects from being printed).
Update the error message for null nodes (which can occur either through a failure to find or through attempting to access a null node like the parent of the root)
Add extra checks for missing files when calling .translate() to prevent segfaulting.

Scientific Software - Peer-reviewed - Cython
Published by jmcbroome over 3 years ago

This update includes the following: 1. New functions for computing relative entropy across the tree for sample-level categorical values, as if it was a decision tree trying to predict those categorical labels. 2. Direct support for arbitrary branch length values, allowing BTE to work with mutation-annotated likelihood or timetrees with specific branch length values. 3. Removal of timer on calling functions that may be called many times in an analysis, such as depthfirstexpansion. 4. Updates to handling of annotation labels. 5. Various bugfixes and improved exception handling.

Full Changelog: https://github.com/jmcbroome/BTE/compare/v0.8.1...v0.8.2

Scientific Software - Peer-reviewed - Cython
Published by jmcbroome over 3 years ago

BTE - Documentation and QOL

This release is mostly focused on updates to documentation, including the following:

Docstrings for functions which return lists of bytes (UTF-8 encoded strings) are corrected
There is a new check preventing the user from attempting to access the parent of the root node, which could easily lead to segmentation faults
Most error messaging has been redirected from stdout to stderr, allowing the user to more easily control logging behavior by redirection
The function "mutationset" has been renamed to "gethaplotype", which more clearly describes its function, along with a general rewriting of its docstring. The old name is still usable, with a deprecation warning, and will be removed in the next major release.

Additionally, there is one new function, dumpannotations(), which returns a dictionary mapping all currently annotated lineages and the nodes they are associated with; this is the inverse operation of the existing applyannotations() function.