Issues

• Add support for recombination maps and new mismatch approach

  tskit-dev/tsinfer#1199 · Filter by author Duncan-JR opened on Oct 2, 2026

• Automatically filter out singletons/multi-allelics before ancestor inference

  tskit-dev/tsinfer#1198 · Filter by author Duncan-JR opened on Oct 2, 2026

• Validate source compatibility before merging by position

  tskit-dev/tsinfer#1197 · Filter by author Duncan-JR opened on Oct 2, 2026

• VCZ inference uses the first declared contig instead of the variants' contig

  bug
  tskit-dev/tsinfer#1196 · Filter by author Duncan-JR opened on Oct 2, 2026

• Numpy value error

  tskit-dev/tsinfer#1193 · Filter by author Zedthedrifter opened on Aug 27, 2026
  6

• Apply site filters before constructing MultiSourceView

  tskit-dev/tsinfer#1192 · Filter by author Duncan-JR opened on Aug 19, 2026
  1

• Need a flag to decide what to do about sites that are not shared between multiple VCZ input files

  tskit-dev/tsinfer#1190 · Filter by author hyanwong opened on Jul 24, 2026
  5

• Reimplement support for sites with multiple mutations

  tskit-dev/tsinfer#1186 · Filter by author hyanwong opened on Jun 10, 2026
  2

• pipeline.match exposes reference_ts / config [match].reference_ts but always builds make_root_ts instead

  tskit-dev/tsinfer#1185 · Filter by author hyanwong opened on Jun 8, 2026
  6

• Update to use vcztools 0.2.0

  tskit-dev/tsinfer#1184 · Filter by author jeromekelleher opened on Jun 8, 2026
  

• Moving breakpoints by mapping non-inference mutations

  tskit-dev/tsinfer#1183 · Filter by author hyanwong opened on May 13, 2026

• Add "align_edges" operation

  tskit-dev/tsinfer#1179 · Filter by author jeromekelleher opened on Mar 31, 2026
  4

• Implement distributed commands

  tskit-dev/tsinfer#1175 · Filter by author jeromekelleher opened on Mar 30, 2026
  1

• Add tests for coordinate overflow

  tskit-dev/tsinfer#1170 · Filter by author jeromekelleher opened on Mar 27, 2026

• Implement path_compression

  tskit-dev/tsinfer#1169 · Filter by author jeromekelleher opened on Mar 27, 2026
  1

• Validate multi-ancestor approaches at scale

  tskit-dev/tsinfer#1167 · Filter by author jeromekelleher opened on Mar 27, 2026
  5

• Run "unified genealogy" inferences and test multi-source inference

  tskit-dev/tsinfer#1166 · Filter by author jeromekelleher opened on Mar 27, 2026
  2

• Update documentation for 1.0 changes

  tskit-dev/tsinfer#1164 · Filter by author jeromekelleher opened on Mar 27, 2026

• Remove references to sgkit

  tskit-dev/tsinfer#1107 · Filter by author hyanwong opened on Mar 3, 2026

• Fixup build check for numba

  tskit-dev/tsinfer#1097 · Filter by author jeromekelleher opened on Feb 26, 2026
  1

• Add numa pip install option

  tskit-dev/tsinfer#1085 · Filter by author jeromekelleher opened on Feb 17, 2026

• Minor simplification of docs with newer tskit2zarr version

  tskit-dev/tsinfer#1075 · Filter by author hyanwong opened on Feb 6, 2026

• Compiler warnings

  tskit-dev/tsinfer#1069 · Filter by author jeromekelleher opened on Jan 30, 2026
  3

  

• Expose force_sample_times in .infer()

  tskit-dev/tsinfer#1033 · Filter by author hyanwong opened on Jun 20, 2025

• Docs: replace "genealogy" with "ARG" globally?

  tskit-dev/tsinfer#1026 · Filter by author jeromekelleher opened on Mar 31, 2025 · Release 0.4.2
  4