8000 Commits · EI-CoreBioinformatics/mikado · GitHub

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Commits

Commits on Sep 3, 2021

Version 2.3.2
ljyanesm
committed

Commits on Sep 1, 2021

Commits on Aug 19, 2021

Merge branch 'perf_issue_ONT_MT' into add_transcripts_method
lucventurini
authored
Reorganised, often by breaking down in more manageable functions, some of the abstractlocus parts.
Luca Venturini
committed
Silly bug in previous commit, fixed here
Luca Venturini
committed
Code cleaning
Luca Venturini
committed
BugFix for the segment trees for the transcript. Trying to improve result storer
Luca Venturini
committed
Use sorted lists to avoid checking all the ancestors/descendants of an intron
ljyanesm
committed
Cosmetic changes
Luca Venturini
committed
WiP: unit-tests pass.
Luca Venturini
committed

Commits on Aug 18, 2021

Kinda solved the issue and also split the add_transcripts into 'safe' and 'unsafe'
Luca Venturini
committed
Still BROKEN, one of the unit-tests still fails.
Luca Venturini
committed
First partially broken implementation of the new method
Luca Venturini
committed

Commits on Aug 17, 2021

Removed as much as possible the single-removal of transcripts from the loci classes. Resolved the breaking bug.
Luca Venturini
committed
WIP Removing transcripts
ljyanesm
committed
Added a test to ensure that swapping transcripts with the same number of introns and exons will trigger the locus segment tree recalculation.
Luca Venturini
committed
Removing the mandatory recalculation after adding/removing and instead making sure that the segmenttree gets *properly* checked to verify that it needs to be recalculated.
Luca Venturini
committed
Small bugfix for keeping reference transcripts when doing the padding
Luca Venturini
committed
Forcing segmenttree calculation when adding a transcript to the locus/
Luca Venturini
committed
Fixed the previous commit, specifically the __getstate__ method was broken
Luca Venturini
committed
Actually fixed the underlying issue ...
Luca Venturini
committed
This fixes the issue for good *but* is a bit of a cheat
Luca Venturini
committed

Commits on Aug 16, 2021

WIP Missing intron from graph
ljyanesm
committed
Fixed the extraction script and added some show-stoppers
Luca Venturini
committed
WIP Missing intron from graph
ljyanesm
committed

Commits on Aug 13, 2021

Fixed the padding hopefully
Luca Venturini
committed
Small quick cleaning up
Luca Venturini
committed

Commits on Aug 12, 2021

Fixes extract_test_case.py
ljyanesm
committed

Commits on Aug 10, 2021

Add script to extract test cases
ljyanesm
committed

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