ivan-krukov aligning-genealogies issues

ivan-krukov / aligning-genealogies

The genealogy-coalescent alignment project

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Bump certifi from 2020.4.5.2 to 2022.12.7

#45 dependabot[bot] opened 1 year ago
0
Bump nbconvert from 5.6.1 to 6.5.1

#44 dependabot[bot] opened 2 years ago
0
Bump nbconvert from 5.6.1 to 6.3.0

#43 dependabot[bot] closed 2 years ago
1
Bump mistune from 0.8.4 to 2.0.3

#42 dependabot[bot] opened 2 years ago
0
Bump numpy from 1.18.5 to 1.22.0

#41 dependabot[bot] opened 2 years ago
0
Bump notebook from 6.0.3 to 6.4.12

#40 dependabot[bot] opened 2 years ago
0
Bump notebook from 6.0.3 to 6.4.10

#39 dependabot[bot] closed 2 years ago
1
Bump ipython from 7.15.0 to 7.16.3

#38 dependabot[bot] opened 2 years ago
0
Bump notebook from 6.0.3 to 6.4.1

#37 dependabot[bot] closed 2 years ago
1
Bump urllib3 from 1.25.9 to 1.26.5

#36 dependabot[bot] opened 3 years ago
0
Bump bleach from 3.1.5 to 3.3.0

#35 dependabot[bot] opened 3 years ago
0
Bump py from 1.8.2 to 1.10.0

#34 dependabot[bot] opened 3 years ago
0
Bump pygments from 2.6.1 to 2.7.4

#33 dependabot[bot] opened 3 years ago
0
Bump jinja2 from 2.11.2 to 2.11.3

#32 dependabot[bot] opened 3 years ago
0
Bump notebook from 6.0.3 to 6.1.5

#31 dependabot[bot] closed 3 years ago
1
Incorporate inferred tree sequences to the software

#30 shz9 opened 4 years ago
4
Drawing for HaplotypeGraph

#29 shz9 opened 4 years ago
0
Convert traversal to tree sequences

#28 ivan-krukov opened 4 years ago
0
Unify logic for dealing with ploidy

#27 shz9 opened 4 years ago
3
Incorporate path completion to greedy Aligners

#26 shz9 opened 4 years ago
0
Add notebooks for coalescence events check

#25 andjelatodorovic closed 4 years ago
0
Travis CI

#24 ivan-krukov closed 4 years ago
0
Diploid visualization

#23 ivan-krukov closed 4 years ago
1
Re-write `get_probands_under` method

#22 shz9 closed 4 years ago
1
Add kinship aligner into the `Aligner` interface

#21 ivan-krukov opened 4 years ago
0
`Pedigree.sample_path` does not work

#20 ivan-krukov closed 4 years ago
1
Time-aware Pedigree climbling

#19 ivan-krukov opened 4 years ago
1
Simulations should assign sex to individuals

#18 ivan-krukov closed 4 years ago
1
Test everything

#17 ivan-krukov opened 4 years ago
0
Add harmonization step to Aligner objects

#16 shz9 opened 4 years ago
6
Add detailed documentation to methods in main classes

#15 shz9 opened 4 years ago
1
Add focused view to .draw() methods

#14 shz9 closed 4 years ago
1
Update sample_path to account for ploidy

#13 shz9 closed 4 years ago
2
Specific updates to visualization methods

#12 shz9 closed 4 years ago
2
Matching IDs in genealogy and the tree sequence

#11 ivan-krukov closed 4 years ago
6
`Genealogical.predecessors` no longer has `include_self`

#10 ivan-krukov closed 4 years ago
1
Project structure

#9 ivan-krukov closed 4 years ago
0
Simulate with example BALSAC data

#8 ivan-krukov closed 4 years ago
2
Visualization

#7 ivan-krukov opened 4 years ago
0
Implement greedy climbing

#6 ivan-krukov opened 4 years ago
1
Implement Ancestral concordance metric

#5 sgravel opened 4 years ago
0
Write tree sequence to genealogy alignment object

#4 sgravel opened 4 years ago
0
Link with msprime simulations, so that we can directly simulate+ evaluate

#3 sgravel closed 4 years ago
5
Aligner should handle node to edge matchings

#2 sgravel opened 4 years ago
1
Do not inherit directly from nx.DiGraph

#1 ivan-krukov closed 4 years ago
1