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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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Redirect for docs object.inv
#238
benjeffery
closed
2 years ago
1
inconsistent time scaling after calling pyslim.recapitate
#237
bguo068
closed
2 years ago
1
Error in VCF output: More than 9 alleles not currently supported
#235
mariharris
closed
2 years ago
3
docs update (closes #139)
#234
petrelharp
closed
2 years ago
0
use samples(time=) for individuals_alive_at sometimes (closes #208)
#233
petrelharp
closed
2 years ago
0
clean up requirements and test with windows?
#232
petrelharp
closed
2 years ago
3
halfway deprecations
#231
petrelharp
closed
2 years ago
1
deprecate SlimTreeSequence
#230
petrelharp
closed
2 years ago
1
removed legacy metadata (closes #219)
#229
petrelharp
closed
2 years ago
1
update requirements
#228
petrelharp
closed
2 years ago
0
deprecate `ts.slim_generation`
#227
petrelharp
closed
2 years ago
1
use unique names in phylo vignette
#226
petrelharp
closed
2 years ago
1
add `mutation_rate` to recapitate
#225
petrelharp
closed
2 years ago
3
More updates
#224
petrelharp
closed
2 years ago
1
fixup XY annotation example
#223
petrelharp
opened
2 years ago
0
mention time units
#222
petrelharp
closed
2 years ago
2
load.pyslim leads to "AttributeError: can't set attribute" after upgrade
#221
ChrystelleDelord
closed
2 years ago
4
test running `.py` files in SLiM recipes
#220
petrelharp
opened
2 years ago
2
remove legacy metadata
#219
petrelharp
closed
2 years ago
1
change `generate_nucleotides` to use reference sequence if present
#218
petrelharp
closed
2 years ago
0
check v3.6 files
#217
petrelharp
closed
2 years ago
0
switch to new reference sequence
#216
petrelharp
closed
2 years ago
1
citation.cff (closes #188)
#215
petrelharp
opened
2 years ago
0
Release tasks
#214
petrelharp
closed
2 years ago
0
remove `./circleci`
#213
petrelharp
closed
2 years ago
1
Vignettes as "tutorials" on tskit.dev/tutorials?
#212
hyanwong
opened
2 years ago
1
monitor memory and do gc
#211
petrelharp
closed
2 years ago
2
String encoding error in util.py/pack_bytes
#210
barytonos
closed
2 years ago
18
use `table.metadata_vector( )` in docs
#209
petrelharp
opened
2 years ago
0
switch to using `ts.samples(time=X)` in examples?
#208
petrelharp
closed
2 years ago
1
adjust to new individual metadata
#207
bhaller
closed
2 years ago
1
adjust to new nucleotide reference sequence location
#206
bhaller
closed
2 years ago
1
Fix typos
#205
xin-huang
closed
2 years ago
1
Cannot replicate the example in extracting-information-about-selected-mutations
#204
xin-huang
closed
2 years ago
2
add `samples_only` argument to `individuals_alive_at`
#203
petrelharp
closed
2 years ago
1
add _X and _Y tests
#202
petrelharp
opened
2 years ago
0
Fixing union vignette
#201
mufernando
closed
2 years ago
7
fixup of union vignette
#200
petrelharp
closed
2 years ago
3
fix union vignette - counting samples in union-ed tree sequence
#199
mufernando
closed
2 years ago
0
removed nonexistent argument from docs: closes #196
#197
petrelharp
closed
2 years ago
1
individual_parents() not accepting array of individual ID's
#196
pam-alamilla
closed
2 years ago
4
tutorial for tracking lineages across space
#195
petrelharp
opened
2 years ago
0
add methods like popsizes to docs
#194
petrelharp
closed
2 years ago
0
redirect docs to tskit.dev
#193
petrelharp
closed
2 years ago
3
WIP Union vignette
#190
mufernando
closed
2 years ago
8
population_size method
#189
petrelharp
closed
3 years ago
5
add citation.cff
#188
petrelharp
opened
3 years ago
0
add method to compute discretized population density
#186
giliapatterson
closed
3 years ago
0
individual_populations gives *birth* locations, not sampling locations
#185
petrelharp
closed
2 years ago
1
update to tutorial.md to take a sample of individuals, check node IDs
#184
chriscrsmith
closed
3 years ago
2
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