Issues

• to_zarr then from_zarr drops the phased flag, so a saved simulation comes back unphased

  kr-colab/pg_gpu#403 · Filter by author andrewkern opened on Nov 7, 2026

• from_vcf pairs sites across contig boundaries when no region= is given

  kr-colab/pg_gpu#398 · Filter by author nspope opened on Nov 6, 2026

• multiple device support?

  kr-colab/pg_gpu#388 · Filter by author molpopgen opened on Nov 4, 2026
  2

• dd and pi2 raise AttributeError for a tuple n_valid, and dd(i, j) reads the tuple by position

  kr-colab/pg_gpu#384 · Filter by author andrewkern opened on Nov 4, 2026

• Windowed mean_r2 and ld_decay raise TypeError by default, and ld_max_distance has no effect

  kr-colab/pg_gpu#383 · Filter by author andrewkern opened on Nov 4, 2026
  1

• SFS functions return None on a stream over a region with no variants

  kr-colab/pg_gpu#382 · Filter by author andrewkern opened on Nov 4, 2026

• sfs_folded_scaled(stream, population=...) raises NotImplementedError; sfs_folded on the same stream works

  kr-colab/pg_gpu#381 · Filter by author andrewkern opened on Nov 4, 2026

• plot_pairwise_ld, plot_joint_sfs and plot_ld_decay fail or drop data on valid inputs

  kr-colab/pg_gpu#380 · Filter by author andrewkern opened on Nov 4, 2026

• average_patterson_f3 and average_patterson_d raise ZeroDivisionError when the SE is 0 or when 'exclude' leaves no site

  kr-colab/pg_gpu#379 · Filter by author andrewkern opened on Nov 4, 2026

• f3 with normed=False counts sites where f3 cannot be estimated as 0, so the mean is biased toward 0

  kr-colab/pg_gpu#378 · Filter by author andrewkern opened on Nov 4, 2026

• windowed_statistics het_expected counts sites with fewer than two calls as 0

  kr-colab/pg_gpu#377 · Filter by author andrewkern opened on Nov 4, 2026

• Scalar max_daf uses sites with one call; windowed max_daf skips them

  kr-colab/pg_gpu#376 · Filter by author andrewkern opened on Nov 4, 2026

• Scalar pi, theta_w, theta_h, theta_l (and dxy, da under 'exclude') give 0.0 for a region with no accessible base

  kr-colab/pg_gpu#374 · Filter by author andrewkern opened on Nov 4, 2026

• Local PCA decides window validity from the wrong count: before the 'exclude' filter, and in one-hot columns for the jackknife

  kr-colab/pg_gpu#373 · Filter by author andrewkern opened on Nov 4, 2026

• FrequencySpectrum pi and Watterson are 2x the scalar at a two-allele site without the reference allele

  kr-colab/pg_gpu#372 · Filter by author andrewkern opened on Nov 4, 2026

• HaplotypeMatrix.n_segregating_sites sums allele codes and misses multiallelic sites

  kr-colab/pg_gpu#371 · Filter by author andrewkern opened on Nov 4, 2026

• fold_sfs and fold_joint_sfs give wrong bins for an even number of chromosomes

  kr-colab/pg_gpu#370 · Filter by author andrewkern opened on Nov 4, 2026

• daf_histogram and windowed daf_hist put a fixed-derived site in the top bin; the docs and sfs leave it out

  kr-colab/pg_gpu#369 · Filter by author andrewkern opened on Nov 4, 2026

• daf_histogram on a GenotypeMatrix bins monomorphic and no-call sites at frequency 0 and ignores missing_data

  kr-colab/pg_gpu#368 · Filter by author andrewkern opened on Nov 4, 2026

• ihs and xpehh with map_pos and missing_data='exclude' raise IndexError or use the wrong gaps

  kr-colab/pg_gpu#367 · Filter by author andrewkern opened on Nov 4, 2026
  1

• xpnsl and xpehh with missing_data='exclude' drop sites for missing calls in populations they do not read

  kr-colab/pg_gpu#366 · Filter by author andrewkern opened on Nov 4, 2026
  1

• moments_ld.compute_ld_statistics ignores accessible_bed when the input is a matrix

  kr-colab/pg_gpu#365 · Filter by author andrewkern opened on Nov 4, 2026

• is_accessible in windowed_statistics and windowed_statistics_fused is one base off at each mask edge

  kr-colab/pg_gpu#364 · Filter by author andrewkern opened on Nov 4, 2026
  1

• A BED file with more than one contig is merged into one mask when no chrom is given

  kr-colab/pg_gpu#363 · Filter by author andrewkern opened on Nov 4, 2026

• zx total ZnS uses every row of the matrix, and under 'exclude' the three terms use different sites

  kr-colab/pg_gpu#362 · Filter by author andrewkern opened on Nov 4, 2026