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pangenome
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odgi
Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
https://doi.org/10.1093/bioinformatics/btac308
MIT License
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is there a way to extract from a graph with uncompacted node IDs?
#497
esrice
opened
1 year ago
0
Overeager link-adding in `odgi flip`
#496
anshumanmohan
opened
1 year ago
2
Strange behavior in `odgi build`
#495
anshumanmohan
opened
1 year ago
7
Portability fixes to build with Clang, on macOS, and on ARM
#494
sampsyo
closed
1 year ago
3
Race condition in ".pathnames.iv" file in position command
#493
ASLeonard
opened
1 year ago
12
`odgi overlap`: fix header
#492
AndreaGuarracino
closed
1 year ago
0
Towards a 2D RG-PG-SGD
#491
subwaystation
opened
1 year ago
3
fix a bug with reference-guided PG-SGD
#490
subwaystation
closed
1 year ago
0
atomicbitvector assertion error in untangle
#489
esrice
opened
1 year ago
2
`odgi paths` allows a specific occurrence of the delimiter
#488
AndreaGuarracino
closed
1 year ago
0
Odgi 1d visualization: understanding several drawn links to the very end of the image
#487
henrivkgt
opened
1 year ago
1
Untangly cleanup v2
#486
ekg
opened
1 year ago
0
`odgi flip`: avoid introducing useless edges and losing edges from the original graph
#485
AndreaGuarracino
closed
1 year ago
1
Inconsistent matrix generation in `odgi paths`
#484
sivico26
closed
1 year ago
5
`odgi paths`: initialize vector values
#483
AndreaGuarracino
closed
1 year ago
0
Fix versioning
#482
AndreaGuarracino
closed
1 year ago
0
Python API function divide_handle() can not get the offsets list input
#481
hahahafeifeifei
opened
1 year ago
2
Optimization of zeta preprocessing
#480
nsmlzl
closed
1 year ago
2
Specify the path color
#479
minglibio
opened
1 year ago
5
`odgi extract` is frustrating
#478
subwaystation
opened
1 year ago
1
Approach combining "odgi depth / odgi extract" with "vg deconstruct" VERSUS the approach based on the BubbleGun algorithm for genotyping pangenome graphs: potential inconsistency between these two approaches?
#477
diaspj
opened
1 year ago
1
`odgi inject`: use a key that is really unique across annotations
#476
AndreaGuarracino
closed
1 year ago
2
odgi inject with overlapping bed entries
#475
henrivkgt
closed
1 year ago
11
prevent quadratic untangle cut point explosions
#474
ekg
opened
1 year ago
10
fix smoothxg-offending import
#473
AndreaGuarracino
closed
1 year ago
0
script to generate release binaries
#472
subwaystation
closed
1 year ago
1
fix the iteration bound: now the iter_max we set is the exact running iteration
#471
tonyjie
closed
1 year ago
0
[odgi tension] Set the distance to 0 after each step instead of each path
#470
tonyjie
closed
1 year ago
1
`odgi untangle`: verbose log
#469
AndreaGuarracino
closed
1 year ago
0
`odgi stepindex`: unsampled step index
#468
AndreaGuarracino
closed
1 year ago
0
add yaml output for -j -w when all paths are emitted
#467
subwaystation
closed
1 year ago
0
ensure that the optimal sum_of_path_node_distances is actually 1
#466
subwaystation
closed
1 year ago
1
`odgi unchop`: avoid merging the same node multiple times
#465
AndreaGuarracino
closed
1 year ago
0
Error with ODGI Extract
#464
brettChapman
opened
1 year ago
1
collapse/combine/edit path names of existing graph?
#463
dduchen
opened
1 year ago
1
Fix segfault when no progress flag set
#462
nsmlzl
closed
1 year ago
1
[odgi::extract] error: no path to fully retain.
#461
ld9866
closed
1 year ago
0
`odgi extract`: avoid creating subgraphs with empty subpaths; `odgi prune`: remove empty paths
#460
AndreaGuarracino
closed
2 years ago
0
Increment progress-meter of `odgi layout` less frequent
#459
AndreaGuarracino
closed
2 years ago
0
Increment progress-meter of odgi sort less frequent
#458
nsmlzl
closed
2 years ago
1
optionally scale haplotype matrix cells by node length
#457
ekg
closed
2 years ago
0
always emit long version format
#456
AndreaGuarracino
closed
2 years ago
0
How to understand PAV ratio?
#455
Yutang-ETH
closed
1 year ago
1
A sampled step index implementation of the PG-SGD algorithm
#454
subwaystation
opened
2 years ago
0
Fix position to print all paths for all bed regions
#453
ASLeonard
opened
2 years ago
0
non-binary halotype matrix
#452
ekg
closed
2 years ago
1
A new odgi function wish, odgi synteny, or a syntenywish...?
#451
diaspj
opened
2 years ago
0
path keep, path drop
#450
ekg
closed
2 years ago
0
privvg: log1p frequency for smoother behavior
#449
ekg
closed
2 years ago
0
implement privvg algorithm
#448
ekg
closed
2 years ago
0
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