Issues

• Need to split edges higher up the hierarchy

  tskit-dev/sc2ts#619 · Filter by author hyanwong opened on Jul 17, 2026
  2

• Point to the analysis repo in README

  tskit-dev/sc2ts#612 · Filter by author szhan opened on Jun 8, 2026

• Viridian dataset missing metadata description fields

  tskit-dev/sc2ts#579 · Filter by author jeromekelleher opened on Nov 21, 2025
  1

• Add sphinx-click output to docs without warnings

  tskit-dev/sc2ts#576 · Filter by author jeromekelleher opened on Nov 20, 2025

• Remove usage of "strain", replace with "sample_id"

  tskit-dev/sc2ts#574 · Filter by author jeromekelleher opened on Nov 20, 2025

• Standardise repo along tskit-dev projects

  tskit-dev/sc2ts#572 · Filter by author jeromekelleher opened on Nov 20, 2025

• Warning in Python 3.13: unclosed database in <sqlite3.Connection object>

  tskit-dev/sc2ts#534 · Filter by author hyanwong opened on Aug 14, 2025

• Use comparison with Usher to fine-tune

  tskit-dev/sc2ts#520 · Filter by author jeromekelleher opened on Jul 6, 2025

• Only read in necessary sample chunks in Dataset.variants()

  enhancement
  tskit-dev/sc2ts#517 · Filter by author jeromekelleher opened on Jul 3, 2025

• Add adjust breakpoints to postprocessing.

  tskit-dev/sc2ts#482 · Filter by author jeromekelleher opened on Mar 4, 2025
  1

• Add ruff linting

  tskit-dev/sc2ts#446 · Filter by author jeromekelleher opened on Dec 13, 2024
  

• Add some prints at the start of infer

  tskit-dev/sc2ts#442 · Filter by author jeromekelleher opened on Dec 12, 2024

• Document infer command and toml format

  tskit-dev/sc2ts#439 · Filter by author jeromekelleher opened on Dec 12, 2024

• Replace node report Markdown with Panel

  tskit-dev/sc2ts#437 · Filter by author jeromekelleher opened on Dec 8, 2024

• Cleaup node_report header

  tskit-dev/sc2ts#435 · Filter by author jeromekelleher opened on Dec 7, 2024

• Cannot convert numpy types to json (numpy 2.0)

  tskit-dev/sc2ts#433 · Filter by author hyanwong opened on Dec 4, 2024

• Future work: weighting HMM matching by mutational probability

  tskit-dev/sc2ts#431 · Filter by author hyanwong opened on Dec 4, 2024
  2

• Alternative approach to encoding deletions

  tskit-dev/sc2ts#367 · Filter by author hyanwong opened on Oct 14, 2024

• Fix earliest_date for unknown lineages

  tskit-dev/sc2ts#303 · Filter by author jeromekelleher opened on Sep 25, 2024

• Add TreeInfo tool to report on retrospective matches

  tskit-dev/sc2ts#296 · Filter by author jeromekelleher opened on Sep 24, 2024

• pango_recombinant_lineages_report is misleading

  tskit-dev/sc2ts#111 · Filter by author jeromekelleher opened on Mar 3, 2023

• Classification for non-biological reversions

  tskit-dev/sc2ts#100 · Filter by author jeromekelleher opened on Feb 12, 2023
  13

• Add site_summary data frame

  tskit-dev/sc2ts#98 · Filter by author jeromekelleher opened on Feb 10, 2023
  1

• Classifying reversion mutations

  tskit-dev/sc2ts#94 · Filter by author hyanwong opened on Feb 8, 2023
  1

• Reversion push code needs to deal with recombinants

  tskit-dev/sc2ts#86 · Filter by author jeromekelleher opened on Feb 6, 2023
  2