v0.3.0

New functionnalities

• correct (WIP, experimental) corrects the graph by adding missing information back into it.
• multigrapher creates interactive graph representation of the differnces between two pangenome graphs
• compress (WIP, experimental) compresses the graph by collapsing substitution bubbles, losselessly
• unfold (WIP, experimental) break cycles in the graph by adding nodes and edges in it

What's Changed

• ✨ Adding cycle breaking unfold command by @Tharos-ux in #18
• 🐛 Fix issue #19, #20 with changes in main and grapher by @Tharos-ux in #21
• 🧵 Adding multithreading on edit by @Tharos-ux in #22
• ⬆️ Fix dependencies and deprecate isolate_by_range.py by @Tharos-ux in #23
• ➖ Fix main.py imports by @Tharos-ux in #24
• 🔊 Add basic logs for edit_distance by @Tharos-ux in #25
• 🐛 Fix typeerror on arg for edition by @Tharos-ux in #26
• ⚡️ Adding low-memory profile for graph loading by @Tharos-ux in #27
• 🔊 Adding logs for edit_distance by @Tharos-ux in #28
• Pattern exclusion, memory tracing and toy examples update by @Tharos-ux in #29
• 📈 Add memory tracking in edit_distance by @Tharos-ux in #30
• Main by @Tharos-ux in #31
• Main by @Tharos-ux in #32
• Main by @Tharos-ux in #33
• 🚑️ Add security on orientation_view accesses by @Tharos-ux in #34
• Adding multigrapher to the palette of tools by @Tharos-ux in #35
• Add timing for HPRC experiment by @Tharos-ux in #36
• ⚡️ Improving performance of pancat edit, pancat grapher and `panc… by @Tharos-ux in #37
• Main by @Tharos-ux in #38
• Build 0.3.0 by @Tharos-ux in #39

Full Changelog: v0.2.0...v0.3.0

v0.2.0

Major update that brings a lot of fixes, new functionalities regarding edition, performance upgrades and more.

General:

• Changed repository name from pangraphs to pancat because pangraph already existed.
• Command line changed (from pangraphs to pancat) for the same reason.
• Many bugfixes (see issues #6, #8, #9 and #12)

Warning

It is mandatory to update the packages tharos-pytools and gfagraphs to their latest version to have the tool working!

Edition:

• Added support for graph-level edition
• Refactoring of the code for the edition, for a huge performance gain

Extraction:

• Removed functions for subgraph extraction as they were buggy on graph with cycles and redundant with some other tools existing elsewhere; will see later if another implementation can be made.

Visualization:

• Adding support for size classes of nodes, fixing bugs on some specific case of graphs with cycles.

Offset annotation:

• Introducing a small update for a loop-aware formalism for the PO tag, along with a new implementation of the function, now moved into the gfagraphs lib (but still usable in command-line nonetheless).

Complete pangenome graph:

• Adding a functionality to assert if a pangenome graph is complete or not (if all input genomes are correctly embed in the graph) : see #7 .

Genome reconstruction:

• Fix of a bug that would have occur on graph with nested loops.

v0.1.1

This version is mostly about bugfixes and solving issues that were underlying (#3). Command-lines were revised accordingly to feedback (see #1, #2) and some new display options were added to grapher (#4).

• Adding boundaries to node size display color and computation
• Adding stats command
• Adding docs for software
• Fix path creation and retrieval
• Removed -g parameter on all commands. Good riddance!

v0.1.0

Initial release, with six functional functions :

• grapher creates interactive graph representation from a GFA file
• reconstruct recreates the linear sequences from the graph
• offset adds relative position information as a tag in GFA file
• isolate extracts a subgraph from positions in the paths
• neigborhood extracts a subgraph from a set of nodes around a node
• edit computes a edit distance between variation graphs

Those are accessible through the command pangraphs.

Other functions are let as scripts, and are located in the scripts folder.