Issues

• write(): Table + annot_tracks fails — Table is not picklable for the loky track jobs

  mcvickerlab/GenVarLoader#423 · Filter by author d-laub opened on Sep 25, 2026

• Public per-variant filter (or a public chunk type) for flat variant windows

  mcvickerlab/GenVarLoader#418 · Filter by author d-laub opened on Sep 16, 2026

• Dataset: no way to clip regions to a sub-interval BED (panel/exome footprints)

  mcvickerlab/GenVarLoader#417 · Filter by author d-laub opened on Sep 16, 2026

• svar2 range probe: fuse the search loop into a Rust kernel

  mcvickerlab/GenVarLoader#404 · Filter by author d-laub opened on Sep 15, 2026
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• streaming: re-aligned tracks disagree with the written path when with_len(L) exceeds a deletion-shrunk haplotype's natural length

  type: bug
  mcvickerlab/GenVarLoader#398 · Filter by author d-laub opened on Sep 13, 2026

• cargo clippy -D warnings and cargo fmt --check are red on the crate baseline

  type: enhancement
  mcvickerlab/GenVarLoader#396 · Filter by author d-laub opened on Sep 13, 2026

• extend_to_length is a no-op on the PGEN writer path (VCF and PGEN datasets disagree)

  type: bug
  mcvickerlab/GenVarLoader#386 · Filter by author d-laub opened on Sep 11, 2026

• streaming: clear pre-existing clippy debt in src/

  type: enhancement
  mcvickerlab/GenVarLoader#384 · Filter by author d-laub opened on Sep 9, 2026

• streaming: jitter with tracks (tracks-only, then mixed + realign)

  type: enhancement
  mcvickerlab/GenVarLoader#383 · Filter by author d-laub opened on Sep 9, 2026

• streaming: derive TRACK_BYTES_PER_CELL from a real interval-density sample

  type: enhancement
  mcvickerlab/GenVarLoader#382 · Filter by author d-laub opened on Sep 9, 2026

• streaming: document that base_seed is batching-dependent for FlankSample

  type: documentation
  mcvickerlab/GenVarLoader#381 · Filter by author d-laub opened on Sep 9, 2026

• streaming: GIL-free track producer (gate on measurement)

  type: enhancement
  mcvickerlab/GenVarLoader#378 · Filter by author d-laub opened on Sep 9, 2026

• streaming: annot_tracks= support

  type: enhancement
  mcvickerlab/GenVarLoader#377 · Filter by author d-laub opened on Sep 9, 2026

• streaming: parity against extend_to_length=True and max_jitter>0

  type: enhancement
  mcvickerlab/GenVarLoader#376 · Filter by author d-laub opened on Sep 9, 2026

• Get the full test suite under 5 minutes

  type: enhancement
  mcvickerlab/GenVarLoader#372 · Filter by author d-laub opened on Sep 9, 2026

• Batched Dataset[r_arr, s_arr] attaches re-aligned tracks to the wrong rows when n_tracks > 1

  type: bug
  mcvickerlab/GenVarLoader#371 · Filter by author d-laub opened on Sep 9, 2026

• Dataset.n_variants() returns zeros on SVAR2 datasets

  mcvickerlab/GenVarLoader#363 · Filter by author d-laub opened on Sep 8, 2026

• _output_bytes_per_instance under-charges one offset entry per offsets array

  mcvickerlab/GenVarLoader#362 · Filter by author d-laub opened on Sep 8, 2026

• ci: cache tests/data/1kg so a Zenodo outage can't red the whole matrix

  type: enhancement
  mcvickerlab/GenVarLoader#360 · Filter by author d-laub opened on Sep 8, 2026

• Parallelism configuration is env-var-only: no way to force parallelism off, and no in-code override

  type: enhancement
  mcvickerlab/GenVarLoader#352 · Filter by author d-laub opened on Sep 6, 2026

• perf: gvl.concat holds one file handle per input — exceeds ulimit -n when merging many shards

  mcvickerlab/GenVarLoader#345 · Filter by author d-laub opened on Jul 31, 2026

• test: gvl.concat has no svar2 coverage — add an .svar2 concat fixture

  mcvickerlab/GenVarLoader#343 · Filter by author d-laub opened on Jul 31, 2026

• _write_from_svar (SVAR1) ignores max_mem

  mcvickerlab/GenVarLoader#342 · Filter by author d-laub opened on Jul 31, 2026

• Shrink the SVAR2 on-disk range cache below 16 bytes/entry

  mcvickerlab/GenVarLoader#341 · Filter by author d-laub opened on Jul 31, 2026

• perf: bulk dataset IO should use buffered read/write, not np.memmap — ~5-6x slower on NFSv3

  mcvickerlab/GenVarLoader#338 · Filter by author d-laub opened on Jul 31, 2026
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