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tskit-dev
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pyslim
Tools for dealing with tree sequences coming to and from SLiM.
MIT License
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23
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fix for dependency graph
#183
petrelharp
closed
2 years ago
1
edited tutorial.md to take a sample of individuals
#182
chriscrsmith
closed
3 years ago
3
Fix pickling of SlimTreeSequence
#181
benjeffery
closed
3 years ago
2
Unpickling TreeSequence from pyslim doesn't initialize metadata, and raises exception
#180
vsbuffalo
closed
3 years ago
4
add method to get the largest SLiM mutation ID
#179
petrelharp
closed
1 year ago
3
add example of converting to nucleotides for VCF output
#178
petrelharp
closed
1 year ago
0
Add doc deps
#177
benjeffery
closed
3 years ago
0
regenerate example tree sequences
#176
petrelharp
closed
3 years ago
1
add example of getting the correct individuals
#175
petrelharp
closed
2 years ago
1
method to convert alleles to nucleotides
#174
petrelharp
closed
3 years ago
13
migration to being functional
#173
petrelharp
closed
2 years ago
4
make sure we don't set `slim_generation` property
#172
petrelharp
closed
2 years ago
0
write example of finding the realised DFE
#171
petrelharp
closed
2 years ago
1
deal with `first()` stages
#170
petrelharp
closed
2 years ago
3
wrap union to deal with SLiM metadata
#169
mufernando
opened
3 years ago
4
provide method to remap alleles (eg for VCF output)
#168
petrelharp
closed
3 years ago
14
annotate fails on empty tree sequence
#167
petrelharp
closed
2 years ago
0
deal appropriately when annotating with existing mutations
#166
petrelharp
closed
2 years ago
0
add tests for weird handcrafted ts behavior
#163
petrelharp
closed
2 years ago
3
change default maximum spatial extent to 1.0
#162
petrelharp
closed
2 years ago
0
add test that verifies default annotations can be loaded in for spatial sims
#161
petrelharp
closed
2 years ago
0
test SLiM population metadata with names for pops
#159
petrelharp
closed
2 years ago
0
dynamically generate and cache `.individual_ages` etcetera
#156
petrelharp
closed
2 years ago
1
setup docs on tskit.dev
#155
petrelharp
closed
2 years ago
1
Switch docs to jupyterbook and update to msprime v1 in the process
#154
petrelharp
closed
3 years ago
1
change migration example in docstring for recapitate
#153
petrelharp
closed
2 years ago
0
add example of using "retain" in the tutorial
#152
petrelharp
opened
3 years ago
0
version bump
#151
petrelharp
closed
3 years ago
0
test on release slim also
#150
petrelharp
closed
3 years ago
1
slim file version bump
#149
petrelharp
closed
3 years ago
0
fixup recapitate passing of recombination_map
#148
petrelharp
closed
3 years ago
2
move `reference_sequence` to metadata?
#147
petrelharp
closed
2 years ago
2
github CI?
#146
petrelharp
closed
3 years ago
0
switch to .github/workflows from .circleci
#145
petrelharp
opened
3 years ago
2
removed discrete msprime hack: closes #141
#144
petrelharp
closed
3 years ago
2
improve test of mutation time
#143
petrelharp
closed
3 years ago
1
Correct old terminology
#142
hyanwong
closed
3 years ago
0
Release that works with current msprime 1.0 alpha
#141
jeromekelleher
closed
3 years ago
5
make reference page for what's in the metadata
#139
petrelharp
closed
2 years ago
0
Define attributes in Sphinx to allow linking
#138
hyanwong
closed
2 years ago
1
Jupyter-book format, SLiM cell magic
#137
hyanwong
closed
3 years ago
4
update links to tskit documentation to tskit.dev
#136
petrelharp
closed
3 years ago
1
'SlimTreeSequence' object has no attribute 'individual_parents'
#135
raeckel
closed
3 years ago
3
Make test suite names match those in SLiM treerec tests?
#134
hyanwong
closed
2 years ago
6
look into missing restart_and_run tests
#133
petrelharp
closed
2 years ago
2
msprime.simulate() doesn't support `discrete_genome` param.
#132
grahamgower
closed
3 years ago
3
Refactor tests
#131
hyanwong
closed
3 years ago
10
_table_metadata_schemas
#130
Arslan-Zaidi
closed
3 years ago
0
space vignette fixup
#129
petrelharp
closed
3 years ago
0
fixup vignette
#128
petrelharp
closed
3 years ago
0
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