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Update dev requirements

Infrastructure and toolsDevelopment infrastructure and toolsDevelopment infrastructure and tools

Status: Open.

#3134 In tskit-dev/tskit;

· agladstein opened on Apr 3, 2025

String encoding in structured metadata arrays

Status: Open.

#3097 In tskit-dev/tskit;

· benjeffery opened on Mar 7, 2025

CI time

Status: Open.

#3026 In tskit-dev/tskit;

· benjeffery opened on Oct 16, 2024

Unifying stat method desc and linking to math summary

Status: Open (in progress).

tskit-dev/tskitnumber 3005

#3005 In tskit-dev/tskit;

· gregorgorjanc opened on Sep 28, 2024

time windows in statistics

Status: Draft (not ready).

tskit-dev/tskitnumber 2948

#2948 In tskit-dev/tskit;

· petrelharp opened on May 9, 2024

Implement efficient seeking from non-null trees using tree_pos

Status: Draft (not ready).

tskit-dev/tskitnumber 2911

#2911 In tskit-dev/tskit;

· duncanMR opened on Feb 26, 2024

write_vcf should use the reference sequence for REF, if present

Status: Open.

#2898 In tskit-dev/tskit;

· hyanwong opened on Feb 7, 2024

Add tests for genotype imputation

Status: Open (in progress).

tskit-dev/tskitnumber 2815

#2815 In tskit-dev/tskit;

· szhan opened on Aug 7, 2023

Remove legacy h5py based formats

Status: Open.

#2812 In tskit-dev/tskit;

· benjeffery opened on Aug 3, 2023

Remove tsk_diff_iter_t

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

Status: Open.

#2797 In tskit-dev/tskit;

· jeromekelleher opened on Jul 13, 2023

Update stats API algorithms to use tree_position_t

Status: Open.

#2796 In tskit-dev/tskit;

· jeromekelleher opened on Jul 13, 2023

Add parallelism to stats API

enhancementNew feature or requestNew feature or request

Status: Open.

#2784 In tskit-dev/tskit;

· jeromekelleher opened on Jul 7, 2023

Support windows in stats API that do not span whole genome

enhancementNew feature or requestNew feature or request

Status: Open.

#2782 In tskit-dev/tskit;

· jeromekelleher opened on Jul 7, 2023

Document divergence_matrix

documentationDocumentationDocumentation

Status: Open.

#2781 In tskit-dev/tskit;

· jeromekelleher opened on Jul 7, 2023

Add support for <code>individuals</code> to divergence_matrix

enhancementNew feature or requestNew feature or request

Status: Open.

#2780 In tskit-dev/tskit;

· jeromekelleher opened on Jul 7, 2023

Add docs discussing how to get a matrix of pairwise comparisons

Status: Open (in progress).

tskit-dev/tskitnumber 2776

#2776 In tskit-dev/tskit;

· hyanwong opened on Jul 5, 2023

Generic iterator class for trees and variants

Status: Draft (not ready).

tskit-dev/tskitnumber 2762

#2762 In tskit-dev/tskit;

· hyanwong opened on Jun 13, 2023

Update docs for improved seek-from-null performance

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

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

Status: Open.

#2740 In tskit-dev/tskit;

· jeromekelleher opened on Apr 14, 2023

Error if boolean passed as row index or slice?

enhancementNew feature or requestNew feature or request

Status: Open.

#2705 In tskit-dev/tskit;

· benjeffery opened on Feb 2, 2023

Document RateMap etc

Status: Open.

#2679 In tskit-dev/tskit;

· hyanwong opened on Jan 10, 2023

Make tqdm(ts.variants()) work better

enhancementNew feature or requestNew feature or request

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

Status: Open.

#2625 In tskit-dev/tskit;

· jeromekelleher opened on Nov 2, 2022

Memory profiling

Infrastructure and toolsDevelopment infrastructure and toolsDevelopment infrastructure and tools

Status: Open.

#2457 In tskit-dev/tskit;

· benjeffery opened on Aug 4, 2022

Check VCF output for conformance with VCF 4.3 and update version number

enhancementNew feature or requestNew feature or request

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

Status: Open.

#2449 In tskit-dev/tskit;

· jeromekelleher opened on Jul 29, 2022

Use MetadataTable to implement metadata functionality

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

refactoringIssue is about refactoring existing codeIssue is about refactoring existing code

Status: Open.

#2440 In tskit-dev/tskit;

· jeromekelleher opened on Jul 25, 2022

Implement state machine for tsk_variant_t and keep reference to <code>tree_sequence</code> in restricted_copy.

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

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

Status: Open.

#2436 In tskit-dev/tskit;

· jeromekelleher opened on Jul 25, 2022