Issues

• 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• windowed_statistics is largely superceded by windowed_analysis, is documented inconsistently, and is another route for bugs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
  3

• 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

• Windowed Garud H does not treat missing genotypes as wildcards

  bug
  kr-colab/pg_gpu#303 · 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

• Latent diversity / SFS statistic bugs

  bug
  kr-colab/pg_gpu#272 · Filter by author nspope opened on Sep 4, 2026

• tally_gpu_haplotypes overflows when a variant pair has more than 127 shared haplotypes

  bug
  kr-colab/pg_gpu#269 · Filter by author nspope opened on Sep 3, 2026

• distance_based_stats disagrees with dd() on dd1/dd2 under missing data

  bug
  kr-colab/pg_gpu#267 · Filter by author nspope opened on Sep 3, 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

• Chromosome bounds from a region differ between the VCF and zarr loaders

  bug
  kr-colab/pg_gpu#231 · Filter by author andrewkern opened on Aug 25, 2026
  2

  

• 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
  2

• 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

• Eager zarr readers copy the genotype block twice

  cleanup
  kr-colab/pg_gpu#194 · 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

• return number of accessible bases in windowed_analysis

  enhancement
  kr-colab/pg_gpu#171 · Filter by author mufernando opened on Aug 6, 2026

• windowed_analysis does not support GenotypeMatrix

  enhancement
  kr-colab/pg_gpu#170 · Filter by author mufernando opened on Aug 5, 2026
  1

• PCA on genotypes

  enhancement
  kr-colab/pg_gpu#169 · Filter by author mufernando opened on Aug 3, 2026
  4