tskit-dev/tskit

Issues

• Adding to SVG output

  #3086 opened a month ago by hyanwong
  9

• `allele_frequency_spectrum` with a 1-d sample set throws uninformative error

  #3083 opened 2 months ago by petrelharp
  1

• Documentation/Tutorial for multithreading

  #3078 opened 2 months ago by hanbin973
  4

• Map mutations using Sankoff's algorithm

  #3071 opened 3 months ago by hyanwong
  0

• Cannot remove nodes using ts.simplify()

  #3057 opened 4 months ago by jcsokol
  16

• allow a different set of nodes for the "right hand side" on `genetic_relatedness_vector`

  #3062 opened 4 months ago by petrelharp
  0

• `pair_coalescence_rate` doesn't account for empty regions (e.g. flanks)

  #3053 opened 4 months ago by hyanwong
  2

• `ts.pair_coalescence_counts` truncates output array dimension to last time window with a node

  #3046 opened 4 months ago by nspope
  0

• `genetic_relatedness` thinks it needs 2 samples sets but is valid with only one

  #3055 opened 4 months ago by petrelharp
  0

• Document that inverting `pair_coalescence_rate` should account for factor of 2 to match diploid Ne

  #3054 opened 4 months ago by hyanwong
  0

• (Undocumented) pack_untracked_polytomies option not correctly identifying branches to pack

  #3049 opened 5 months ago by hyanwong
  1

• `ts.pair_coalescence_rates` can give large or infinite rates

  #3048 opened 5 months ago by hyanwong
  2

• Avoid unnecessary upwards traversals in `tsk_pair_coalescence_stat`

  #3047 opened 5 months ago by nspope
  0

• spatial locations outside of population bounds

  #3041 opened 5 months ago by ShyamieG
  1

• provide feedback on `max_iter` for `extend_haplotypes`

  #2988 opened 6 months ago by petrelharp
  5

• pair_coalescence_rates fails with overall time window [0, float('inf')] and sometimes also with [0, 20000, 100000, float('inf')]

  #3035 opened 5 months ago by Luker121
  5

• Extra HTML tags in provenance summary

  #3039 opened 5 months ago by jeromekelleher
  0

• CI time

  #3026 opened 5 months ago by benjeffery
  9

• Properly document `rf_distance`

  #2992 opened 5 months ago by benjeffery
  1

• Update changelog for 0.5.9

  #2994 opened 5 months ago by benjeffery
  4

• Python 3.13

  #3030 opened 5 months ago by benjeffery
  0

• add a docs section discussing operations with the relatedness matrix

  #3020 opened 5 months ago by petrelharp
  0

• Values as comma-separated thousands

  #3017 opened 5 months ago by savitakartik
  1

• Polytomy collapsing

  #3011 opened 6 months ago by hyanwong
  5

• draw_svg y_ticks doc issues and unexpected behaviour

  #2990 opened 6 months ago by jeromekelleher
  8

• allow `genetic_relatedness_vector` to take non-sample nodes

  #2998 opened 6 months ago by petrelharp
  0

• Ability to add tick positions and annotations to the X axis in draw_svg()

  #3000 opened 6 months ago by hyanwong
  2

• include windows in `genetic_relatedness_vector`

  #2996 opened 6 months ago by petrelharp
  2

• set default for genetic_relatedness to polarised=True and remove a factor of 1/2

  #2981 opened 6 months ago by petrelharp
  2

• Trivial wording change

  #2977 opened 6 months ago by hyanwong
  1

• allow `mode="mutation"` for `genetic_relatedness_vector` (and make this default?)

  #2997 opened 6 months ago by petrelharp
  0

• Add XTable.drop_metadata

  #2944 opened a year ago by jeromekelleher
  1

• Update GitHub upload/download artefacts

  #2943 opened a year ago by jeromekelleher
  0

• Clarification on pairwise coalescent rates

  #2986 opened 6 months ago by Luker121
  12

• inconsistent handling of non-ancestral material in non-strict, unpolarised branch stats

  #2983 opened 6 months ago by petrelharp
  2

• wrong output for genetic_relatedness(... indexes=None, proportion=True)

  #2984 opened 6 months ago by petrelharp
  0

• "mutation" mode for statistics

  #2982 opened 7 months ago by petrelharp
  1

• clarify that genetic_relatedness includes self comparisons

  #2978 opened 7 months ago by petrelharp
  1

• keep_intervals() giving _tskit.LibraryError: Can't squash, flush, simplify or link ancestors...

  #2936 opened 8 months ago by TymekPieszko
  7

• Cannot pickle '_tskit.Tree' object

  #2971 opened 8 months ago by Silloky
  3

• edges lost after merging two trees

  #2929 opened 9 months ago by ShyamieG
  20

• Pass a numpy array of booleans to python simplify?

  #2968 opened 9 months ago by hyanwong
  7

• Fix tests for numpy 2.0

  #2963 opened 9 months ago by jeromekelleher
  1

• Post release for 0.5.7

  #2961 opened 9 months ago by jeromekelleher
  1

• Fixup tests for lshmm 0.0.6

  #2962 opened 9 months ago by jeromekelleher
  7

• Drop "benchmark" CI job?

  #2965 opened 9 months ago by jeromekelleher
  0

• trees.c Compilation Error

  #2950 opened 10 months ago by micailamarcelle
  2

• Split large numbers in html/cli print out.

  #2951 opened 10 months ago by benjeffery
  0

• Folded AFS between branch and site modes differs by factor of two

  #2925 opened a year ago by nspope
  7

• Codecov upload issues

  #2931 opened a year ago by benjeffery
  1