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Add 'mutation' mode

Status: Closed (abandoned).

tskit-dev/tskitnumber 3314

#3314 In tskit-dev/tskit;

· by petrelharp was closed on Nov 17, 2025

Tolerate invalid parents when computing mutation parents

Status: Merged (completed).

tskit-dev/tskitnumber 3309

#3309 In tskit-dev/tskit;

· by benjeffery was closed on Nov 4, 2025

Add isolated_as_missing to ts.alignements

Status: Closed (abandoned).

tskit-dev/tskitnumber 3294

#3294 In tskit-dev/tskit;

· by benjeffery was closed on Nov 10, 2025

Remove guard against internal samples when decoding genotypes

Status: Closed (abandoned).

tskit-dev/tskitnumber 3301

#3301 In tskit-dev/tskit;

· by benjeffery was closed on Nov 10, 2025

Allow internal nodes when isolate_as_missing

Status: Merged (completed).

tskit-dev/tskitnumber 3313

#3313 In tskit-dev/tskit;

· by benjeffery was closed on Nov 11, 2025

Missingness support in alignments

Status: Merged (completed).

tskit-dev/tskitnumber 3317

#3317 In tskit-dev/tskit;

· by benjeffery was closed on Nov 12, 2025

Alignments using C API

Status: Merged (completed).

tskit-dev/tskitnumber 3326

#3326 In tskit-dev/tskit;

· by benjeffery was closed on Nov 25, 2025

Documentation/Consistency Review

Status: Merged (completed).

tskit-dev/tskitnumber 3329

#3329 In tskit-dev/tskit;

· by benjeffery was closed on Nov 24, 2025

Add link-ancestors to TreeSequence and ImmutableTableCollection

Status: Merged (completed).

tskit-dev/tskitnumber 3312

#3312 In tskit-dev/tskit;

· by benjeffery was closed on Nov 26, 2025

Nasty gotcha in the AFS calculation - mutation parents

Status: Closed (completed).

#2729 In tskit-dev/tskit;

· by lukashuebner was closed on Sep 23, 2025

Require mutation parents for TreeSequence instantiation

enhancementNew feature or requestNew feature or request

Status: Closed (completed).

#2732 In tskit-dev/tskit;

· by jeromekelleher was closed on Sep 23, 2025

<code>compute_mutation_parents</code> errors when existing mutation parents don't make sense

bugSomething isn't workingSomething isn't working

Status: Closed (completed).

#3303 In tskit-dev/tskit;

· by petrelharp was closed on Nov 4, 2025

Drop "benchmark" CI job?

Infrastructure and toolsDevelopment infrastructure and toolsDevelopment infrastructure and tools

Status: Closed (completed).

#2965 In tskit-dev/tskit;

· by jeromekelleher was closed on Jun 15, 2025

New tskit.jit module

enhancementNew feature or requestNew feature or request

Status: Closed (completed).

#3135 In tskit-dev/tskit;

· by jeromekelleher was closed on Sep 22, 2025

MetadataSchema doesn't validate the schema

enhancementNew feature or requestNew feature or request

Python APIIssue is about the Python APIIssue is about the Python API

Status: Closed (completed).

#2102 In tskit-dev/tskit;

· by jeromekelleher was closed on Nov 5, 2025

assigning to <code>ts.tables.metadata</code> does not produce an error message - need read only tables

bugSomething isn't workingSomething isn't working

Python APIIssue is about the Python APIIssue is about the Python API

Status: Closed (completed).

#1906 In tskit-dev/tskit;

· by petrelharp was closed on Nov 4, 2025

Mutation's "inherited" state

enhancementNew feature or requestNew feature or request

futureIssues that are closed as they are not planned in the medium-term, but which are still desirable.Issues that are closed as they are not planned in the medium-term, but which are still desirable.

Python APIIssue is about the Python APIIssue is about the Python API

Status: Closed (completed).

#2631 In tskit-dev/tskit;

· by jeromekelleher was closed on Sep 24, 2025

Add tree sequence initialization flag for "compute mutation parents"

Status: Closed (completed).

#2757 In tskit-dev/tskit;

· by daikitag was closed on Sep 23, 2025

Add <code>isolated_as_missing</code> and <code>contig_id</code> to map_to_vcf_model

Status: Closed (completed).

#3177 In tskit-dev/tskit;

· by jeromekelleher was closed on Jun 16, 2025

Allow duplicate nodes in tsk_variant_init

Status: Closed (completed).

#3323 In tskit-dev/tskit;

· by benjeffery was closed on Nov 19, 2025

Isolated as missing perf

Status: Not planned (skipped).

#3318 In tskit-dev/tskit;

· by benjeffery was closed on Nov 13, 2025

Enable <code>alignments</code> on sc2ts ARG internal nodes

Status: Closed (completed).

#3293 In tskit-dev/tskit;

· by jeromekelleher was closed on Nov 25, 2025

Metadata can appear to be set directly, but doesn't work: unfriendly to the user

enhancementNew feature or requestNew feature or request

Python APIIssue is about the Python APIIssue is about the Python API

Status: Not planned (skipped).

#993 In tskit-dev/tskit;

· by hyanwong was closed on Jun 6, 2025

Support missing data in alignments

bugSomething isn't workingSomething isn't working

Status: Closed (completed).

#1896 In tskit-dev/tskit;

· by jeromekelleher was closed on Nov 12, 2025

Perform check for mutation parent integrity while checking tree integrity

C APIIssue is about the C APIIssue is about the C API

PerformanceThis issue addresses performance, either runtime or memoryThis issue addresses performance, either runtime or memory

Status: Closed (completed).

#3218 In tskit-dev/tskit;

· by jeromekelleher was closed on Nov 10, 2025