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NaN's in ld_matrix output with "ghost" alleles

Status: Open.

#3474In tskit-dev/tskit;

· nspope opened on Aug 5, 2026

cache top-level metadata?

Status: Open.

#3472In tskit-dev/tskit;

· petrelharp opened on Jul 9, 2026

Clarify write_vcf docs, and allow empty individuals list to be passed

Status: Open.

#3463In tskit-dev/tskit;

· hyanwong opened on Jun 9, 2026

Incorrect normalisation in TreeSequence.pair_coalescence_counts (and TreeSequence.pair_coalescence_rates) with isolated samples

Status: Open.

#3459In tskit-dev/tskit;

· nspope opened on May 15, 2026

Simplifying when keeping unary nodes but excluding input roots

Status: Open.

#3450In tskit-dev/tskit;

· hyanwong opened on Apr 25, 2026

Calculating the matrix of pairwise coalescence rates efficiently (with genetic_relatedness_vector)

Status: Open.

#3444In tskit-dev/tskit;

· nspope opened on Apr 2, 2026

PCA fails sometimes (maybe if nodes are not 0...n?)

Status: Open.

#3443In tskit-dev/tskit;

· petrelharp opened on Apr 2, 2026

nans in ld_matrix

Status: Open.

#3441In tskit-dev/tskit;

· petrelharp opened on Mar 22, 2026

developer doc: ninja build fails with CUnit header problems

Status: Open.

#3434In tskit-dev/tskit;

· bhaller opened on Mar 12, 2026

developer doc: meson commands could be more helpful

Status: Open.

#3433In tskit-dev/tskit;

· bhaller opened on Mar 12, 2026

developer doc: meson setup build fails with an error about cunit

Status: Open.

#3432In tskit-dev/tskit;

· bhaller opened on Mar 12, 2026

developer doc sends me into detached head state

Status: Open.

#3431In tskit-dev/tskit;

· bhaller opened on Mar 12, 2026