Issues

• Several scalar statistics return 0.0, not NaN, when too few sites define them

  bug
  kr-colab/pg_gpu#342 · Filter by author andrewkern opened on Oct 20, 2026

• Diversity and divergence statistics count sites with no data as invariant sites

  bug
  kr-colab/pg_gpu#341 · Filter by author andrewkern opened on Oct 20, 2026

• max_daf(missing_data='exclude') returns -1.0 when no site is complete

  bug
  kr-colab/pg_gpu#340 · Filter by author andrewkern opened on Oct 20, 2026

• grm treats a missing genotype as the mean and divides every pair by the total SNP count

  bug
  kr-colab/pg_gpu#339 · Filter by author andrewkern opened on Oct 20, 2026

• Hudson FST and Da are biased upward when a population has only one call at a site

  bug
  kr-colab/pg_gpu#338 · Filter by author andrewkern opened on Oct 20, 2026

• genetic_relatedness treats a missing call as allele frequency 0

  bug
  kr-colab/pg_gpu#337 · Filter by author andrewkern opened on Oct 20, 2026

• dist_moments computes the distance moments with NumPy on the host

  cleanup
  kr-colab/pg_gpu#336 · Filter by author andrewkern opened on Oct 20, 2026

• windowed_analysis ignores window_type and regions for statistics that the scatter and fused engines compute

  bug
  kr-colab/pg_gpu#335 · Filter by author andrewkern opened on Oct 12, 2026
  

• Fused engines copy the matrix under missing_data='exclude', which defeats the chunked engine's memory bound

  bug
  kr-colab/pg_gpu#333 · Filter by author andrewkern opened on Oct 11, 2026

• Lower the peak memory of the pairwise r2 builders

  enhancement
  kr-colab/pg_gpu#325 · Filter by author andrewkern opened on Oct 2, 2026

• HaplotypeMatrix.pairwise_r2's normalization tail dominates its memory footprint

  kr-colab/pg_gpu#323 · Filter by author nspope opened on Oct 1, 2026
  2

• Pairwise distances report 0.0 for a pair with no shared called site

  bug
  kr-colab/pg_gpu#322 · Filter by author andrewkern opened on Oct 1, 2026

• windowed_statistics is largely superceded by windowed_analysis, is documented inconsistently, and is another route for bugs

  cleanup
  kr-colab/pg_gpu#305 · Filter by author nspope opened on Sep 14, 2026
  4

• Fused windowed engine's theta_w (and tajimas_d's numerator) ignore missing data

  bug
  kr-colab/pg_gpu#304 · Filter by author nspope opened on Sep 14, 2026

• Missing-data checks materialize a matrix-sized boolean before reducing

  cleanup
  kr-colab/pg_gpu#301 · Filter by author andrewkern opened on Sep 11, 2026

• Cleanup: the haplotype branch of _stream_n_ind in relatedness is unreachable

  cleanup
  kr-colab/pg_gpu#299 · Filter by author nspope opened on Sep 11, 2026

• Consolidate tests along thematic lines

  infrastructure
  kr-colab/pg_gpu#292 · Filter by author nspope opened on Sep 10, 2026

• r^2 estimators under differential missingness

  bug
  kr-colab/pg_gpu#273 · Filter by author nspope opened on Sep 5, 2026

• Remove the inert gpu_memory_limit / chunk_size params from WindowedAnalyzer

  cleanup
  kr-colab/pg_gpu#260 · Filter by author andrewkern opened on Sep 3, 2026

• test_scikit_allel_comparison_runs_small flakes (subprocess timeout) under host load

  infrastructure
  kr-colab/pg_gpu#252 · Filter by author andrewkern opened on Sep 1, 2026

• Engines disagree on the undefined-FST sentinel and on single-population columns in mixed requests

  bug
  kr-colab/pg_gpu#200 · Filter by author andrewkern opened on Aug 23, 2026
  4

• locate_unlinked syncs to the host once per sliding window

  cleanup
  kr-colab/pg_gpu#196 · Filter by author andrewkern opened on Aug 22, 2026

• check_diploid_encoding allocates several times the genotype block on the host

  cleanup
  kr-colab/pg_gpu#195 · Filter by author andrewkern opened on Aug 22, 2026

• implementing --wagh flag for xp-ehh calculation

  enhancement
  kr-colab/pg_gpu#190 · Filter by author hmsnell opened on Aug 18, 2026
  1

• Unify window membership: _build_scatter_indices and the fused per-site block are two implementations of one rule

  cleanup
  kr-colab/pg_gpu#183 · Filter by author andrewkern opened on Aug 14, 2026