Issue 421: Fix alignment coverage >1.0 and aniM symmetrical behaviour#425

Merged

widdowquinn merged 42 commits intomasterfrom issue_421

Apr 8, 2024

+614,436-166

Commits on Feb 23, 2024

update issue 340
widdowquinn
committed
update Markdown summary of issue_340
widdowquinn
committed
add explainer for delta-filter
widdowquinn
committed
Progress on issue 340

Angelika Kiepas
authored and
widdowquinn
committed
add notebook example of how indels/overlaps affect MUMmer AlignedBases
widdowquinn
committed
add documentation

Angelika Kiepas
authored and
widdowquinn
committed
add scripts&pytest for AlignedBases calculations

Angelika Kiepas
authored and
widdowquinn
committed
incongruency investigation

Angelika Kiepas
authored and
widdowquinn
committed
check nucmer symmetry

kiepczi
authored and
widdowquinn
committed
check nucmer symmetry

kiepczi
authored and
widdowquinn
committed
add draft scipt for A:B and B:A comparisions

kiepczi
authored and
widdowquinn
committed
modify anim.py to get 2 comparisions

kiepczi
authored and
widdowquinn
committed
add reverse comparison to nucmer in pyani 0.3+
widdowquinn
committed
modify anim calculations to exclude overlaps using IntervalTree

kiepczi
authored and
widdowquinn
committed
move intervaltree from pip to conda requirements
widdowquinn
committed
update types in parse_delta()
widdowquinn
committed

Commits on Feb 29, 2024

Update matrices and run tables for forward and reverse comparisons
kiepczi
committed

Commits on Mar 1, 2024

update parse_delta function
kiepczi
committed

Commits on Mar 4, 2024

Update matrices to reflect forward and revese comparisions
kiepczi
committed

Commits on Mar 5, 2024

Commits on Mar 8, 2024

fix %ID calculations to weighted %ID
kiepczi
committed

Commits on Mar 12, 2024

Commits on Mar 15, 2024

Rounding Error Investigation
kiepczi
committed

Commits on Mar 21, 2024

Commits on Mar 25, 2024