tskit-dev tsinfer issues

tskit-dev / tsinfer

Infer a tree sequence from genetic variation data.

GNU General Public License v3.0

56 stars 13 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Document path_or_zarr

#974 hyanwong closed 3 weeks ago
1
Update changelog for 0.4.0a2

#973 benjeffery closed 3 weeks ago
1
Improve test coverage for batch matching

#972 benjeffery opened 3 weeks ago
0
"Ancestral state" or "ancestral allele"?

#971 hyanwong closed 3 weeks ago
2
VariantData parameter name

#970 hyanwong closed 3 weeks ago
1
Remove some test warnings

#969 hyanwong closed 3 weeks ago
1
VariantData: do we want to be able to specify individuals_time on construction?

#968 hyanwong opened 3 weeks ago
2
Remove mention of sgkit

#967 hyanwong closed 3 weeks ago
1
Allow VariantData to take either a vcz path or the zarr store itself

#966 hyanwong closed 3 weeks ago
3
Encode numpy arrays in sample batch json

#965 benjeffery closed 3 weeks ago
2
Deal with multiple contigs and sequence lengths

#964 hyanwong opened 4 weeks ago
2
Properly treat blank ancestral alleles

#963 hyanwong closed 3 weeks ago
8
Do not warn about unknown states if ancestral allele is "N"

#962 hyanwong closed 3 weeks ago
2
Override VariantData.from_tree_sequence

#961 hyanwong closed 3 weeks ago
3
Check for duplicate alleles

#960 hyanwong closed 3 weeks ago
6
Experimental hmm

#959 jeromekelleher opened 4 weeks ago
1
Doc typo

#958 hyanwong closed 4 weeks ago
1
UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.

#957 hyanwong opened 1 month ago
0
Variant data

#956 hyanwong closed 1 month ago
1
Docstring for VariantData needs writing

#955 hyanwong closed 3 weeks ago
1
Refactor batch sample matching

#954 benjeffery closed 4 weeks ago
1
Plot "edge-node time consistency"

#953 hyanwong opened 1 month ago
0
Extra sample nodes being created from .vcz file when ploidies are uneven

#952 hyanwong opened 1 month ago
10
Change readme doc links to "latest"

#951 hyanwong closed 1 month ago
1
Fix wrong schema used for individual metadata

#950 benjeffery closed 1 month ago
1
VariantData sequence_length not being taken from zarr `contig_length` field

#949 hyanwong opened 1 month ago
7
Typo in formats.VariantData.individuals_metadata?

#948 percyfal closed 1 month ago
2
Rename sgkit_sample_id

#947 benjeffery closed 2 months ago
1
Release prep

#946 benjeffery closed 2 months ago
1
Update tutorial for new VariantData format

#945 hyanwong closed 2 months ago
5
VariantData

#944 benjeffery closed 2 months ago
15
Numpy2 changes

#943 hyanwong closed 2 months ago
13
Fix wheel building

#942 benjeffery closed 2 months ago
1
Update CHANGELOG.md

#941 hyanwong closed 2 months ago
2
Specify standard python (not python3)

#940 hyanwong closed 2 months ago
2
Coerce NODE_IS_SAMPLE to correct numpy type before negation

#939 hyanwong closed 2 months ago
3
Incorrect dependencies for package

#938 jeromekelleher closed 2 months ago
2
New bitflag error

#937 hyanwong closed 2 months ago
9
Upgrade actions, build with numpy2

#936 benjeffery closed 2 months ago
5
Numpy 2.0 supporting release

#935 jeromekelleher closed 2 months ago
1
Grep for "sgkit" in names and replace

#934 jeromekelleher closed 3 weeks ago
2
Investigate AFS bias due to polytomies

#933 hyanwong opened 3 months ago
3
Bring sample batch matching in line with ancestor matching

#932 benjeffery opened 3 months ago
0
Set node metadata schema

#931 hyanwong closed 2 months ago
4
Allow the same scheme name, if description matches

#930 hyanwong closed 3 months ago
7
Overwriting md schema

#929 hyanwong closed 3 months ago
0
Always read alleles as strings (not bytes)

#928 hyanwong closed 2 months ago
11
Check all alleles at a site are unique before inference

#927 hyanwong opened 3 months ago
6
Add dependency on tsdate

#926 jeromekelleher opened 4 months ago
3
How to save an SgkitSampleData instance, e.g. for running the CLI

#925 hyanwong opened 4 months ago
4