From 289176afbc530597d70b211a35cd5be35638755a Mon Sep 17 00:00:00 2001
From: d-laub <dlaub@ucsd.edu>
Date: Wed, 16 Sep 2026 05:42:05 -0700
Subject: [PATCH 1/3] perf(svar2): consume genoray's sparse range stream in the
 writer
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

`_write_from_svar2` built its region-CSR cache by materializing genoray's
dense `(samples, ploidy, regions, 2)` chunk and then discarding it: at the
All of Us chr22 grid only 0.45% of `(region, sample, ploid)` windows hold a
variant, the dense intermediate is ~128 GB per contig, and the `np.nonzero`
scan that recovered the useful cells was 71% of the per-chunk kernel.

genoray 4.1.0 emits those cells directly (d-laub/genoray#206), so the scan
and the intermediate both go away. `nonempty_entries` collapses into a CSR
expansion plus four column assignments and is deleted.

The on-disk cache is unchanged, byte for byte. genoray filters on the same
predicate (`end > start` in either channel), emits the same absolute
`slot * ploidy + ploid` cell ids in the same region-major order, and carries
the same raw start with length 0 for a cell non-empty in only one channel.

The nine `_core.run_conversion_pipeline` fixtures move to genoray's
keyword-only, struct-grouped signature (d-laub/genoray#153), which the same
version bump requires.

`nonempty_entries`'s shape check went with it. It guarded a transpose that
no longer exists — the chunk arrives region-major — so the axis order it
defended is now unrepresentable rather than validated. Its int32 cell-id
overflow guard is already enforced by `_SparseWriter`'s `span >= 2**31`
check.

Refs #405.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
---
 python/genvarloader/_dataset/_svar2_ranges.py | 70 +------------------
 python/genvarloader/_dataset/_write.py        | 48 ++++++++-----
 tests/conftest.py                             | 42 ++++++-----
 tests/dataset/conftest.py                     | 21 +++---
 tests/dataset/test_svar2_readbound_diffs.py   | 21 +++---
 tests/dataset/test_svar2_readbound_haps.py    | 21 +++---
 .../dataset/test_svar2_readbound_variants.py  | 21 +++---
 tests/dataset/test_write_svar2.py             | 65 ++++++++++-------
 tests/test_svar2_realign_tracks.py            | 21 +++---
 tests/unit/dataset/test_svar2_ranges.py       | 34 ---------
 10 files changed, 154 insertions(+), 210 deletions(-)

diff --git a/python/genvarloader/_dataset/_svar2_ranges.py b/python/genvarloader/_dataset/_svar2_ranges.py
index 0fbc6735..eb9ec785 100644
--- a/python/genvarloader/_dataset/_svar2_ranges.py
+++ b/python/genvarloader/_dataset/_svar2_ranges.py
@@ -38,7 +38,6 @@
     "_DenseRanges",
     "_ranges_reader",
     "_SparseWriter",
-    "nonempty_entries",
     "merge_region_blocks",
 ]
 
@@ -715,7 +714,8 @@ def append_contig(
     ) -> None:
         """Merge one contig's per-chunk blocks into region-major order and append.
 
-        Each block from :func:`nonempty_entries` is already region-major, and
+        Each block from genoray's sparse range stream is already region-major,
+        and
         chunk ``i``'s sample slots lie entirely below chunk ``i + 1``'s, so the
         merged order is fixed by region alone. That makes this a stable counting
         sort with ``O(rc)`` of auxiliary state, not a comparison sort.
@@ -869,72 +869,6 @@ def close(self) -> int:
         return self.n_entries
 
 
-def nonempty_entries(
-    snp: NDArray[np.int64], indel: NDArray[np.int64], slot0: int, ploidy: int
-) -> tuple[NDArray[np.int32], NDArray[np.int32], NDArray[np.void]]:
-    """Extract non-empty cells from a ``(rc, ns, P, 2)`` pair of range blocks.
-
-    Args:
-        snp: SNP ranges, ``(rc, ns, P, 2)`` -- normally a ``transpose(2, 0, 1, 3)``
-            view of a hap-major genoray chunk.
-        indel: Indel ranges, same shape.
-        slot0: Dataset sample slot of this block's first column.
-        ploidy: ``P``.
-
-    Returns:
-        ``(region, cell, entries)``, region-major: ``region`` is **contig-local**
-        and non-decreasing, ``cell`` is ``slot * ploidy + ploid`` and ascends
-        within each region. Split rather than combined into one key because
-        :meth:`_SparseWriter.append_contig` needs the region axis on its own to
-        count, and ``cell`` is what lands on disk -- combining them would only be
-        undone again.
-
-    Raises:
-        ValueError: If ``snp`` and ``indel`` don't share a shape, or their
-            ploidy axis doesn't match ``ploidy``. A caller that transposes the
-            wrong axes (e.g. swapping the region and sample axes) still
-            produces a same-rank ``(a, b, c, 2)`` array, so this is checked
-            explicitly rather than left to fail downstream -- without it, a
-            mis-transposed cache still writes a self-consistent CSR table
-            with no invariant violated, just region/sample-scrambled entries.
-    """
-    if snp.shape != indel.shape:
-        raise ValueError(
-            "svar2 range cache: snp and indel blocks must share a shape, got"
-            f" {snp.shape} and {indel.shape}"
-        )
-    if snp.ndim != 4 or snp.shape[2] != ploidy:
-        raise ValueError(
-            f"svar2 range cache: expected (regions, samples, ploidy={ploidy}, 2)"
-            f" blocks, got shape {snp.shape}"
-        )
-    ne = (snp[..., 1] > snp[..., 0]) | (indel[..., 1] > indel[..., 0])
-    # np.nonzero walks the LOGICAL shape in C order, so (r, slot, ploid) comes
-    # out ascending even though `ne` is NOT C-contiguous: the `>` above inherits
-    # the transposed view's stride permutation, because numpy allocates ufunc
-    # output with NPY_KEEPORDER. Do not "fix" that with ascontiguousarray --
-    # materializing (rc, ns, P) in C order is a strided scatter costing ~11x the
-    # comparison itself (97.7 ms vs 8.8 ms on a 15e6-cell chunk).
-    ri, sj, pj = np.nonzero(ne)
-    ent = np.empty(len(ri), ENTRY_DTYPE)
-    ent["snp_start"] = snp[ri, sj, pj, 0]
-    ent["snp_len"] = snp[ri, sj, pj, 1] - snp[ri, sj, pj, 0]
-    ent["indel_start"] = indel[ri, sj, pj, 0]
-    ent["indel_len"] = indel[ri, sj, pj, 1] - indel[ri, sj, pj, 0]
-    # Overflow guard local to this function: the sole production call site
-    # (`_write_from_svar2`) already guards `n_samples * ploidy < 2**31` by
-    # constructing `_SparseWriter` first, but `nonempty_entries` is a public
-    # module-level function callable independently of that guard.
-    max_cell = (int(slot0) + int(snp.shape[1]) - 1) * int(ploidy) + int(ploidy) - 1
-    if max_cell > np.iinfo(np.int32).max:
-        raise ValueError(
-            "svar2 range cache: slot0 * ploidy overflows int32"
-            f" (max cell id {max_cell})"
-        )
-    cell = (slot0 + sj).astype(np.int64) * ploidy + pj
-    return ri.astype(np.int32), cell.astype(np.int32), ent
-
-
 def merge_region_blocks(
     readers: "list[_RangeLookup]",
     r_maps: "list[NDArray[np.int64]]",
diff --git a/python/genvarloader/_dataset/_write.py b/python/genvarloader/_dataset/_write.py
index f7d9e5d9..4ace020a 100644
--- a/python/genvarloader/_dataset/_write.py
+++ b/python/genvarloader/_dataset/_write.py
@@ -44,7 +44,7 @@
 from .._variants._utils import path_is_pgen, path_is_vcf
 from ._indexing import s2i
 from ._svar2_link import Svar2Link
-from ._svar2_ranges import ENTRY_DTYPE, _SparseWriter, nonempty_entries
+from ._svar2_ranges import ENTRY_DTYPE, _SparseWriter
 from ._svar_link import SvarLink
 from ._utils import bed_to_regions, regions_to_bed
 
@@ -1267,7 +1267,7 @@ def _write_from_svar2(
             ends = df["chromEnd"].to_numpy()
             # extend_to_length is validated at function entry (False raises); the
             # read-bound kernel sizes haplotype output at read time.
-            stream = svar2._find_ranges_chunked(
+            stream = svar2._find_ranges_chunked_sparse(
                 c, starts, ends, samples=sel, max_mem=max_mem
             )
             dense_snp[lo:hi] = np.asarray(stream.dense_snp_range, np.int64).reshape(
@@ -1290,7 +1290,7 @@ def _write_from_svar2(
                 # append_contig's counting-sort merge assumes chunk i's sample
                 # slots lie entirely below chunk i + 1's (see its docstring): the
                 # merged order is fixed by region alone only because of that.
-                # genoray's `_find_ranges_chunked` happens to yield ascending
+                # genoray's `_find_ranges_chunked_sparse` happens to yield ascending
                 # `sample_start` today, but that is a generator's behaviour in a
                 # separate package, asserted nowhere on either side -- an
                 # out-of-order chunk stream would corrupt the merge silently
@@ -1308,26 +1308,36 @@ def _write_from_svar2(
                         f" {prev_sample_start}."
                     )
                 prev_sample_start = ch.sample_start
-                # Chunks are hap-major (samples, ploidy, regions, 2); transpose to
-                # region-major (regions, samples, ploidy, 2). transpose() is a
-                # view, and nonempty_entries relies on that -- see its comment on
-                # np.nonzero and NPY_KEEPORDER.
-                r, cell, ent = nonempty_entries(
-                    ch.vk_snp_range.transpose(2, 0, 1, 3),
-                    ch.vk_indel_range.transpose(2, 0, 1, 3),
-                    slot0=ch.sample_start,
-                    ploidy=P,
-                )
-                # `nonempty_entries` filters on width, not on genoray's raw start ==
-                # end insertion point (which is what a *dense* cell would carry at
-                # the same coordinate). An all-empty (region, sample, ploid) cell
-                # is therefore never written here, so a real dataset's
+                # The chunk already IS the non-empty set, region-major with
+                # ascending cell_id -- the shape append_contig wants. What used
+                # to stand here was a transpose plus an `np.nonzero` scan over a
+                # dense (samples, ploidy, regions, 2) block, 71% of this kernel
+                # and ~128 GB per All of Us chr22 contig (#405). genoray filters
+                # on the same predicate (`end > start` in either channel) and
+                # emits the same absolute `slot * ploidy + ploid`, so the bytes
+                # written here are unchanged.
+                #
+                # CSR in, region column out: append_contig counts on the region
+                # axis, so expand `region_ptr` rather than make genoray send a
+                # column it would have to build from the same offsets.
+                r = np.repeat(np.arange(rc, dtype=np.int32), np.diff(ch.region_ptr))
+                ent = np.empty(len(ch.cell_id), ENTRY_DTYPE)
+                ent["snp_start"] = ch.snp_start
+                ent["snp_len"] = ch.snp_len
+                ent["indel_start"] = ch.indel_start
+                ent["indel_len"] = ch.indel_len
+                # genoray filters on width, not on its raw start == end insertion
+                # point (which is what a *dense* cell would carry at the same
+                # coordinate). An all-empty (region, sample, ploid) cell is
+                # therefore never written here, so a real dataset's
                 # `_SparseRanges.lookup` always returns (0, 0) for it, never
                 # genoray's insertion point -- unlike `_DenseRanges.lookup`, which
                 # would surface (x, x). That is the one place the two layouts are
-                # not byte-identical (see `_SparseRanges`'s docstring).
+                # not byte-identical (see `_SparseRanges`'s docstring). A cell
+                # non-empty in only ONE channel still carries the other channel's
+                # raw start with length 0, exactly as the dense path produced it.
                 acc_r.append(r)
-                acc_c.append(cell)
+                acc_c.append(ch.cell_id)
                 acc_e.append(ent)
                 np.maximum(keys, ch.max_end_keys, out=keys)
                 pbar.update(rc * ch.n_samples / S)
diff --git a/tests/conftest.py b/tests/conftest.py
index 102b83b8..ac4d2b92 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -185,19 +185,22 @@ def svar2_slot_store(_svar2_slot_src, tmp_path_factory) -> Path:
     leaks into every later consumer of this fixture.
     """
     from genoray import _core
+    from genoray._pipeline_args import FieldSpec, PlanSettings, RegionSpec
 
     bcf, ref = _svar2_slot_src
     store = tmp_path_factory.mktemp("svar2_slot_store") / "store.svar2"
     _core.run_conversion_pipeline(
-        str(bcf),
-        str(ref),
-        ["chr1"],
-        str(store),
-        ["S0", "S1"],
-        25_000,
-        2,
-        1,
-        8 * 1024 * 1024,
+        vcf_path=str(bcf),
+        reference_path=str(ref),
+        output_dir=str(store),
+        regions=RegionSpec(chroms=["chr1"], samples=["S0", "S1"]),
+        fields=FieldSpec(),
+        plan=PlanSettings(
+            chunk_size=25_000,
+            max_threads=1,
+            long_allele_capacity=8 * 1024 * 1024,
+        ),
+        ploidy=2,
     )
     assert (store / "meta.json").exists(), "svar2 conversion did not finish"
     return store
@@ -312,6 +315,7 @@ def _build_svar2(vcf_text: str, samples: list[str], d: Path, name: str) -> Path:
         Path to the finished ``.svar2`` store.
     """
     from genoray import _core
+    from genoray._pipeline_args import FieldSpec, PlanSettings, RegionSpec
 
     ref = d / "ref.fa"
     ref.write_text(f">chr1\n{_SVAR2_REF}\n")
@@ -325,15 +329,17 @@ def _build_svar2(vcf_text: str, samples: list[str], d: Path, name: str) -> Path:
 
     out = d / name
     _core.run_conversion_pipeline(
-        str(bcf),
-        str(ref),
-        ["chr1"],
-        str(out),
-        samples,
-        25_000,
-        2,
-        1,
-        8 * 1024 * 1024,
+        vcf_path=str(bcf),
+        reference_path=str(ref),
+        output_dir=str(out),
+        regions=RegionSpec(chroms=["chr1"], samples=samples),
+        fields=FieldSpec(),
+        plan=PlanSettings(
+            chunk_size=25_000,
+            max_threads=1,
+            long_allele_capacity=8 * 1024 * 1024,
+        ),
+        ploidy=2,
     )
     assert (out / "meta.json").exists(), "conversion did not finish"
     return out
diff --git a/tests/dataset/conftest.py b/tests/dataset/conftest.py
index c26b1acd..6acbe9fd 100644
--- a/tests/dataset/conftest.py
+++ b/tests/dataset/conftest.py
@@ -63,18 +63,21 @@ def vcf_and_ref(tmp_path_factory) -> tuple[Path, Path]:
 def svar2_store(vcf_and_ref, tmp_path_factory) -> Path:
     bcf, ref = vcf_and_ref
     from genoray import _core
+    from genoray._pipeline_args import FieldSpec, PlanSettings, RegionSpec
 
     out = tmp_path_factory.mktemp("svar2_write") / "store.svar2"
     _core.run_conversion_pipeline(
-        str(bcf),
-        str(ref),
-        ["chr1"],
-        str(out),
-        ["S0", "S1", "S2"],
-        25_000,
-        2,
-        1,
-        8 * 1024 * 1024,
+        vcf_path=str(bcf),
+        reference_path=str(ref),
+        output_dir=str(out),
+        regions=RegionSpec(chroms=["chr1"], samples=["S0", "S1", "S2"]),
+        fields=FieldSpec(),
+        plan=PlanSettings(
+            chunk_size=25_000,
+            max_threads=1,
+            long_allele_capacity=8 * 1024 * 1024,
+        ),
+        ploidy=2,
     )
     assert (out / "meta.json").exists(), "conversion did not finish"
     return out
diff --git a/tests/dataset/test_svar2_readbound_diffs.py b/tests/dataset/test_svar2_readbound_diffs.py
index 5504e0c3..ff91a661 100644
--- a/tests/dataset/test_svar2_readbound_diffs.py
+++ b/tests/dataset/test_svar2_readbound_diffs.py
@@ -38,6 +38,7 @@
 @pytest.fixture(scope="module")
 def svar2_store_dense_snp(tmp_path_factory) -> Path:
     from genoray import _core
+    from genoray._pipeline_args import FieldSpec, PlanSettings, RegionSpec
 
     d = tmp_path_factory.mktemp("svar2_readbound_diffs_dense_snp")
     ref = d / "ref.fa"
@@ -52,15 +53,17 @@ def svar2_store_dense_snp(tmp_path_factory) -> Path:
 
     out = d / "store"
     _core.run_conversion_pipeline(
-        str(bcf),
-        str(ref),
-        ["chr1"],
-        str(out),
-        ["S0", "S1"],
-        25_000,
-        2,
-        1,
-        8 * 1024 * 1024,
+        vcf_path=str(bcf),
+        reference_path=str(ref),
+        output_dir=str(out),
+        regions=RegionSpec(chroms=["chr1"], samples=["S0", "S1"]),
+        fields=FieldSpec(),
+        plan=PlanSettings(
+            chunk_size=25_000,
+            max_threads=1,
+            long_allele_capacity=8 * 1024 * 1024,
+        ),
+        ploidy=2,
     )
     assert (out / "meta.json").exists(), "conversion did not finish"
     return out
diff --git a/tests/dataset/test_svar2_readbound_haps.py b/tests/dataset/test_svar2_readbound_haps.py
index a95e9e15..29349494 100644
--- a/tests/dataset/test_svar2_readbound_haps.py
+++ b/tests/dataset/test_svar2_readbound_haps.py
@@ -237,6 +237,7 @@ def test_readbound_matches_union_oracle_with_shifts(svar2_store_2s):
 @pytest.fixture(scope="module")
 def svar2_store_dense_snp(tmp_path_factory) -> Path:
     from genoray import _core
+    from genoray._pipeline_args import FieldSpec, PlanSettings, RegionSpec
 
     d = tmp_path_factory.mktemp("svar2_readbound_dense_snp")
     ref = d / "ref.fa"
@@ -251,15 +252,17 @@ def svar2_store_dense_snp(tmp_path_factory) -> Path:
 
     out = d / "store"
     _core.run_conversion_pipeline(
-        str(bcf),
-        str(ref),
-        ["chr1"],
-        str(out),
-        ["S0", "S1"],
-        25_000,
-        2,
-        1,
-        8 * 1024 * 1024,
+        vcf_path=str(bcf),
+        reference_path=str(ref),
+        output_dir=str(out),
+        regions=RegionSpec(chroms=["chr1"], samples=["S0", "S1"]),
+        fields=FieldSpec(),
+        plan=PlanSettings(
+            chunk_size=25_000,
+            max_threads=1,
+            long_allele_capacity=8 * 1024 * 1024,
+        ),
+        ploidy=2,
     )
     assert (out / "meta.json").exists(), "conversion did not finish"
     return out
diff --git a/tests/dataset/test_svar2_readbound_variants.py b/tests/dataset/test_svar2_readbound_variants.py
index 2389255e..1cf8599f 100644
--- a/tests/dataset/test_svar2_readbound_variants.py
+++ b/tests/dataset/test_svar2_readbound_variants.py
@@ -97,6 +97,7 @@ def test_readbound_variants_match_decode_oracle(svar2_store_2s, regions):
 @pytest.fixture(scope="module")
 def svar2_store_dense_snp(tmp_path_factory) -> Path:
     from genoray import _core
+    from genoray._pipeline_args import FieldSpec, PlanSettings, RegionSpec
 
     d = tmp_path_factory.mktemp("svar2_readbound_variants_dense_snp")
     ref = d / "ref.fa"
@@ -111,15 +112,17 @@ def svar2_store_dense_snp(tmp_path_factory) -> Path:
 
     out = d / "store"
     _core.run_conversion_pipeline(
-        str(bcf),
-        str(ref),
-        ["chr1"],
-        str(out),
-        ["S0", "S1"],
-        25_000,
-        2,
-        1,
-        8 * 1024 * 1024,
+        vcf_path=str(bcf),
+        reference_path=str(ref),
+        output_dir=str(out),
+        regions=RegionSpec(chroms=["chr1"], samples=["S0", "S1"]),
+        fields=FieldSpec(),
+        plan=PlanSettings(
+            chunk_size=25_000,
+            max_threads=1,
+            long_allele_capacity=8 * 1024 * 1024,
+        ),
+        ploidy=2,
     )
     assert (out / "meta.json").exists(), "conversion did not finish"
     return out
diff --git a/tests/dataset/test_write_svar2.py b/tests/dataset/test_write_svar2.py
index ebc5ebfa..73bc5b97 100644
--- a/tests/dataset/test_write_svar2.py
+++ b/tests/dataset/test_write_svar2.py
@@ -71,9 +71,11 @@ def test_write_svar2_emits_cache(svar2_store: Path, tmp_path: Path):
     # independent oracle for this fixture's grid. It does NOT by itself prove a
     # mis-transposed axis order fails loudly here -- `_find_ranges`'s test
     # fixture happens not to distinguish some axis permutations, so that
-    # property is enforced structurally instead, by `nonempty_entries`'s own
-    # shape check (raises on any transpose that changes rank or the ploidy
-    # axis) and pinned end-to-end by tests/dataset/test_svar2_fields_read.py.
+    # property used to be enforced structurally by `nonempty_entries`'s shape
+    # check. Since the writer consumes genoray's sparse stream (#405) there is
+    # no transpose left to get wrong -- the chunk arrives region-major with
+    # absolute cell ids -- so the axis order is now unrepresentable rather than
+    # checked. Still pinned end-to-end by tests/dataset/test_svar2_fields_read.py.
     #
     # It compares WIDTHS and NON-EMPTY entries, not raw bytes: the sparse layout
     # deliberately discards an empty cell's insertion point, which is exactly the
@@ -217,6 +219,7 @@ def test_write_svar2_max_ends_matches_svar1(
 def tie_stores(tmp_path_factory) -> tuple[Path, Path]:
     """Matched .svar2 and .svar stores from the same two-same-POS-records VCF."""
     from genoray import VCF, SparseVar, _core
+    from genoray._pipeline_args import FieldSpec, PlanSettings, RegionSpec
 
     from tests.dataset.conftest import _REF
 
@@ -233,15 +236,17 @@ def tie_stores(tmp_path_factory) -> tuple[Path, Path]:
 
     svar2_out = d / "store.svar2"
     _core.run_conversion_pipeline(
-        str(bcf),
-        str(ref),
-        ["chr1"],
-        str(svar2_out),
-        ["S0", "S1"],
-        25_000,
-        2,
-        1,
-        8 * 1024 * 1024,
+        vcf_path=str(bcf),
+        reference_path=str(ref),
+        output_dir=str(svar2_out),
+        regions=RegionSpec(chroms=["chr1"], samples=["S0", "S1"]),
+        fields=FieldSpec(),
+        plan=PlanSettings(
+            chunk_size=25_000,
+            max_threads=1,
+            long_allele_capacity=8 * 1024 * 1024,
+        ),
+        ploidy=2,
     )
     assert (svar2_out / "meta.json").exists(), "svar2 conversion did not finish"
 
@@ -319,7 +324,7 @@ def test_write_svar2_chunked_matches_unchunked(svar2_store: Path, tmp_path):
     )
 
     calls: list[int] = []
-    real = SparseVar2._find_ranges_chunked
+    real = SparseVar2._find_ranges_chunked_sparse
 
     def spy(self, *args, **kwargs):
         stream = real(self, *args, **kwargs)
@@ -336,11 +341,14 @@ def spy(self, *args, **kwargs):
         overwrite=True,
     )
 
-    SparseVar2._find_ranges_chunked = spy
+    SparseVar2._find_ranges_chunked_sparse = spy
     try:
         small = tmp_path / "small.gvl"
         # 2 regions x ploidy 2 x 2 channels x 2 endpoints x 8 bytes = 128 bytes
-        # per sample; the chunker's own 2x safety margin needs 256 bytes for
+        # per sample. The sparse stream is planned from that same DENSE
+        # per-sample cost (genoray sizes chunks for the worst case, not the
+        # realized fill), so this budget still forces the same split.
+        # The chunker's own 2x safety margin needs 256 bytes for
         # even one sample, so 256 is the smallest budget that both succeeds
         # and forces one-sample-per-chunk (this store has S=2, so that's 2
         # chunks).
@@ -353,7 +361,7 @@ def spy(self, *args, **kwargs):
             overwrite=True,
         )
     finally:
-        SparseVar2._find_ranges_chunked = real
+        SparseVar2._find_ranges_chunked_sparse = real
 
     assert calls and all(c == 1 for c in calls), (
         f"expected one sample per chunk under a 256-byte budget, got {calls}"
@@ -533,18 +541,23 @@ def svar2_store_unsorted(vcf_and_ref, tmp_path_factory) -> Path:
     """
     bcf, ref = vcf_and_ref
     from genoray import _core
+    from genoray._pipeline_args import FieldSpec, PlanSettings, RegionSpec
 
     out = tmp_path_factory.mktemp("svar2_write_unsorted") / "store.svar2"
     _core.run_conversion_pipeline(
-        str(bcf),
-        str(ref),
-        ["chr1"],
-        str(out),
-        ["S1", "S0"],  # reversed vs. the lexicographic order gvl.write emits
-        25_000,
-        2,
-        1,
-        8 * 1024 * 1024,
+        vcf_path=str(bcf),
+        reference_path=str(ref),
+        output_dir=str(out),
+        regions=RegionSpec(
+            chroms=["chr1"], samples=["S1", "S0"]
+        ),  # reversed vs. the lexicographic order gvl.write emits
+        fields=FieldSpec(),
+        plan=PlanSettings(
+            chunk_size=25_000,
+            max_threads=1,
+            long_allele_capacity=8 * 1024 * 1024,
+        ),
+        ploidy=2,
     )
     assert (out / "meta.json").exists(), "conversion did not finish"
     return out
@@ -857,7 +870,7 @@ def test_write_svar2_empty_cell_is_zero_not_insertion_point(
 ):
     """A genuinely empty cell reads back as (0, 0), not genoray's insertion point.
 
-    `nonempty_entries` filters on width, so an all-empty (region, sample, ploid)
+    genoray's sparse stream filters on width, so an all-empty (region, sample, ploid)
     cell is never written. `_SparseRanges.lookup` then returns (0, 0) for it --
     the one place `_SparseRanges` and `_DenseRanges` diverge (see
     `_SparseRanges`'s docstring and the comment in `_write_from_svar2`), since a
diff --git a/tests/test_svar2_realign_tracks.py b/tests/test_svar2_realign_tracks.py
index 0d54f42c..ff07fdea 100644
--- a/tests/test_svar2_realign_tracks.py
+++ b/tests/test_svar2_realign_tracks.py
@@ -33,6 +33,7 @@
 @pytest.fixture(scope="module")
 def svar2_del_store(tmp_path_factory) -> Path:
     from genoray import _core
+    from genoray._pipeline_args import FieldSpec, PlanSettings, RegionSpec
 
     d = tmp_path_factory.mktemp("svar2_del")
     ref = d / "ref.fa"
@@ -47,15 +48,17 @@ def svar2_del_store(tmp_path_factory) -> Path:
 
     out = d / "store"
     _core.run_conversion_pipeline(
-        str(bcf),
-        str(ref),
-        ["chr1"],
-        str(out),
-        ["S0", "S1"],
-        25_000,
-        2,
-        1,
-        8 * 1024 * 1024,
+        vcf_path=str(bcf),
+        reference_path=str(ref),
+        output_dir=str(out),
+        regions=RegionSpec(chroms=["chr1"], samples=["S0", "S1"]),
+        fields=FieldSpec(),
+        plan=PlanSettings(
+            chunk_size=25_000,
+            max_threads=1,
+            long_allele_capacity=8 * 1024 * 1024,
+        ),
+        ploidy=2,
     )
     assert (out / "meta.json").exists(), "conversion did not finish"
     return out
diff --git a/tests/unit/dataset/test_svar2_ranges.py b/tests/unit/dataset/test_svar2_ranges.py
index 20e0962b..5494e29f 100644
--- a/tests/unit/dataset/test_svar2_ranges.py
+++ b/tests/unit/dataset/test_svar2_ranges.py
@@ -924,40 +924,6 @@ def test_append_contig_rejects_out_of_range_cell_id(tmp_path):
     w.close()
 
 
-def test_nonempty_entries_rejects_snp_indel_shape_mismatch():
-    """snp and indel blocks must share a shape.
-
-    A caller that slices or transposes the two channels inconsistently (e.g.
-    a stale sample count on one channel) would otherwise index past one
-    array's bounds or silently pair up unrelated cells -- checked explicitly
-    since both are same-rank, same-dtype arrays that would not otherwise fail
-    fast in `snp[..., 1] > snp[..., 0]`-style broadcasting.
-    """
-    from genvarloader._dataset._svar2_ranges import nonempty_entries
-
-    snp = np.zeros((2, 3, 2, 2), np.int64)
-    indel = np.zeros((2, 4, 2, 2), np.int64)  # samples axis mismatch: 3 vs 4
-    with pytest.raises(ValueError, match="share a shape"):
-        nonempty_entries(snp, indel, slot0=0, ploidy=2)
-
-
-def test_nonempty_entries_rejects_ploidy_axis_mismatch():
-    """The ploidy axis must match the declared `ploidy`.
-
-    Reproduced without this guard: declaring `ploidy=2` against a block whose
-    axis-2 size is actually 3 makes `cell = (slot0 + sj) * ploidy + pj` alias
-    distinct `(sample, ploid)` pairs onto the same cell id -- e.g. cell id 2
-    is emitted by both `(sj=0, pj=2)` and `(sj=1, pj=0)` -- with no error at
-    all, silently merging two samples' variants into one cell.
-    """
-    from genvarloader._dataset._svar2_ranges import nonempty_entries
-
-    snp = np.zeros((2, 3, 3, 2), np.int64)  # real ploidy axis is 3
-    indel = np.zeros((2, 3, 3, 2), np.int64)
-    with pytest.raises(ValueError, match="ploidy"):
-        nonempty_entries(snp, indel, slot0=0, ploidy=2)
-
-
 def test_svar2_n_variants_is_a_zero_stride_view():
     """#355: a dense (R, S, P) int32 of zeros is 50.7 GB at All of Us chr19.
 

From fbfefd119a771a4c982511e59b1cfd45f439aec2 Mon Sep 17 00:00:00 2001
From: d-laub <dlaub@ucsd.edu>
Date: Wed, 16 Sep 2026 05:43:03 -0700
Subject: [PATCH 2/3] build(deps): require genoray >=4.1.0 for the sparse range
 stream

`_write_from_svar2` now calls `SparseVar2._find_ranges_chunked_sparse` and
the test fixtures call the keyword-only `_core.run_conversion_pipeline`.
Neither exists before 4.1.0.

`pixi.lock` is deliberately not regenerated and the `pixi-lock` / `pyrefly`
hooks are skipped for this commit: 4.1.0 is not on PyPI yet, so pixi cannot
resolve this range at all. Run `pixi lock` and re-run the hooks once the
release lands.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
---
 pixi.toml      | 12 +++++++-----
 pyproject.toml |  2 +-
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/pixi.toml b/pixi.toml
index b838d846..f24cabdb 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -102,11 +102,13 @@ numba = "==0.59.1"
 pyarrow = ">=21"
 hirola = "==0.3"
 seqpro = "==0.22.0"
-# genoray >=3.4.0 as the prebuilt abi3 wheel from PyPI — one cp310-abi3 wheel covers
-# py310-313 on both platforms. 3.4.0 carries SparseVar2._find_ranges_chunked, the
-# memory-bounded chunked range API _write_from_svar2 consumes (gvl#333). Mirrors
-# the pyproject range, which spans 3.x and 4.x.
-genoray = ">=3.4.0,<5"
+# genoray >=4.1.0 as the prebuilt abi3 wheel from PyPI — one cp310-abi3 wheel covers
+# py310-313 on both platforms. 4.1.0 carries
+# SparseVar2._find_ranges_chunked_sparse, the sparse chunked range API
+# _write_from_svar2 consumes (gvl#405), and the keyword-only, struct-grouped
+# _core.run_conversion_pipeline the test fixtures call (d-laub/genoray#153).
+# Mirrors the pyproject range.
+genoray = ">=4.1.0,<5"
 polars = "==1.37.1"
 loguru = "*"
 natsort = "*"
diff --git a/pyproject.toml b/pyproject.toml
index 21067747..09b2351e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,7 @@ dependencies = [
     # contig's ranges at once (gvl#333). 4.x is supported: its breaking changes
     # (SparseVar2.from_vcf(tune=) removal, from_vcf_list(max_mem=) semantics)
     # are on APIs GVL never calls.
-    "genoray>=3.4.0,<5",
+    "genoray>=4.1.0,<5",
     "numpy",
     "loguru",
     "natsort",

From 56e7d70eb8b0844aade06555f46c3402771a92bd Mon Sep 17 00:00:00 2001
From: d-laub <dlaub@ucsd.edu>
Date: Wed, 16 Sep 2026 15:11:36 -0700
Subject: [PATCH 3/3] chore(deps): require genoray >=5,<6 and port to
 keyword-only pipeline entry points

genoray 5.0.0 is out, carrying both changes this branch needs: the sparse
range emission from d-laub/genoray#206 and the keyword-only, grouped-argument
pipeline entry points from d-laub/genoray#200. The previous pin
(`>=4.1.0,<5`) anticipated a 4.1.0 that was never cut, so it excludes the
release it was waiting for.

Bump the pin in `pyproject.toml` and `pixi.toml` to `>=5,<6`, relock, and move
both `Cargo.toml` git deps (`svar2-codec`, `genoray_core`) to the 5.0.0 tag
commit 714f876.

5.0.0's breaking changes -- the `GENORAY_*` environment variables, the
`reader_workers=` parameter and `resolve_log_level` -- all land on APIs
genvarloader never calls, so nothing here needed rewriting for them.

What did need rewriting: #200 made the `_core` pipeline entry points
keyword-only and grouped their arguments into `RegionSpec` / `FieldSpec` /
`PlanSettings`. The twelve test call sites that build svar2 fixtures now pass
keywords and those dataclasses instead of a positional argument list.

Re-checked the empty-cell contract at the new rev, as the comment in
`Cargo.toml` asks: `gather_haps_readbound_impl` still consumes every range
purely as a slice bound, so a `len == 0` range's `start` is never
dereferenced.

Full suite against the real 5.0.0 wheel: 1315 passed, 43 skipped, 4 xfailed.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
---
 Cargo.lock                                |   4 +-
 Cargo.toml                                |  15 +-
 pixi.lock                                 | 237 +++++++++++-----------
 pixi.toml                                 |   8 +-
 pyproject.toml                            |  13 +-
 tests/dataset/test_svar2_contig_naming.py |  21 +-
 tests/dataset/test_svar2_dataset.py       |  42 ++--
 7 files changed, 180 insertions(+), 160 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 88f3aab5..937dcf7b 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -501,7 +501,7 @@ dependencies = [
 [[package]]
 name = "genoray"
 version = "0.1.0"
-source = "git+https://github.com/d-laub/genoray.git?rev=d66ec0e03d097fa8c338567b0938924be67315db#d66ec0e03d097fa8c338567b0938924be67315db"
+source = "git+https://github.com/d-laub/genoray.git?rev=714f8761574b0d4e934d18c694dcaadacd946a2d#714f8761574b0d4e934d18c694dcaadacd946a2d"
 dependencies = [
  "bytemuck",
  "crossbeam-channel",
@@ -1479,7 +1479,7 @@ checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
 [[package]]
 name = "svar2-codec"
 version = "0.1.0"
-source = "git+https://github.com/d-laub/genoray.git?rev=d66ec0e03d097fa8c338567b0938924be67315db#d66ec0e03d097fa8c338567b0938924be67315db"
+source = "git+https://github.com/d-laub/genoray.git?rev=714f8761574b0d4e934d18c694dcaadacd946a2d#714f8761574b0d4e934d18c694dcaadacd946a2d"
 
 [[package]]
 name = "syn"
diff --git a/Cargo.toml b/Cargo.toml
index 477109c1..bb7cf0f0 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -22,18 +22,21 @@ seqpro-core = "0.1"
 # genoray crates are pulled straight from GitHub (no crates.io publish). Cargo finds
 # each package by name inside the repo — no in-repo path is given or needed. Bump `rev`
 # to pull newer genoray code; both crates must share the same rev (one clone, one repo).
-# Currently tag 4.0.1. Keep this rev in step with the `genoray` Python pin: the Rust
+# Currently tag 5.0.0. Keep this rev in step with the `genoray` Python pin: the Rust
 # code here reads svar2 stores that the Python package writes, so a format change that
 # lands in one and not the other is invisible until it corrupts a read.
 # `default-features = false` selects genoray's query-only core; since 4.0.1 that also
 # excludes `tracing`/`tracing-subscriber`, which are gated behind its `conversion`
 # feature (d-laub/genoray#165).
 # The sparse range cache's empty-cell contract also depends on this pin:
-# `gather_haps_readbound_impl` (genoray:src/query/gather.rs:772) must never
-# dereference an empty range's `start`, since that's what makes writing `(0, 0)`
-# for an absent cell safe rather than a corrupt read. Re-check this on any bump.
-svar2-codec = { git = "https://github.com/d-laub/genoray.git", rev = "d66ec0e03d097fa8c338567b0938924be67315db" }
-genoray_core = { git = "https://github.com/d-laub/genoray.git", rev = "d66ec0e03d097fa8c338567b0938924be67315db", package = "genoray", default-features = false }
+# `gather_haps_readbound_impl` (genoray:src/query/gather.rs:869 at 5.0.0) must
+# never dereference an empty range's `start`, since that's what makes writing
+# `(0, 0)` for an absent cell safe rather than a corrupt read. Re-check this on
+# any bump. Re-checked at 5.0.0: every range is consumed as a SLICE bound
+# (`d_snp_pos[ss..se]`, `snp_positions[vs..ve]`), so `len == 0` yields an empty
+# slice and the loop body never runs -- the `start` is never dereferenced.
+svar2-codec = { git = "https://github.com/d-laub/genoray.git", rev = "714f8761574b0d4e934d18c694dcaadacd946a2d" }
+genoray_core = { git = "https://github.com/d-laub/genoray.git", rev = "714f8761574b0d4e934d18c694dcaadacd946a2d", package = "genoray", default-features = false }
 
 [features]
 extension-module = ["pyo3/extension-module"]
diff --git a/pixi.lock b/pixi.lock
index 499499dd..c536f9fd 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -1,7 +1,16 @@
 version: 7
 platforms:
 - name: linux-64
+  virtual-packages:
+  - __unix=0=0
+  - __linux=4.18
+  - __glibc=2.28
+  - __archspec=0=x86_64
 - name: osx-arm64
+  virtual-packages:
+  - __unix=0=0
+  - __osx=13.0
+  - __archspec=0=m1
 environments:
   default:
     channels:
@@ -164,7 +173,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/uc-micro-py-2.0.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.7.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda
-      - pypi: .
+      - pypi: ./
       - pypi: https://files.pythonhosted.org/packages/00/ba/8d8aa1df96e0666752e5c9d406d440495df2014d315b2a95bbef9856b23e/datafusion-50.1.0-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/08/75/ec73e38812bca7c2240aff481b9ddff20d1ad2f10dee4b3353f5eeaacdab/polars-1.37.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/0a/59/69032bf511d51bbc2d45311110386042a7b6a62e6149f919e94a1b55979e/pybigwig-0.3.25-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
@@ -191,7 +200,6 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/6b/a4/bd8ad7d1cf66268219f282d4268b6ba73f8ff51c5fba2c9663adab103615/sorted_nearest-0.0.41.tar.gz
       - pypi: https://files.pythonhosted.org/packages/6e/ae/76fb528c6112a3df5a581a18f1a2ceee5983d54977d7f2b6bc883637fe4c/polars_config_meta-0.3.4-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/71/cc/18245721fa7747065ab478316c7fea7c74777d07f37ae60db2e84f8172e8/beartype-0.22.9-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/73/48/8980acebec96c6615639e44471e00023f15274ce027e485805b0c8b49280/genoray-4.0.1-cp310-abi3-manylinux_2_28_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/74/ff/9d30128a88df6c795097b6f73218d4a5afcd0e2d74cf2dedd99b28d42cdc/cyvcf2-0.31.4-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/78/b6/6307fbef88d9b5ee7421e68d78a9f162e0da4900bc5f5793f6d3d0e34fb8/annotated_types-0.7.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/79/7b/2c79738432f5c924bef5071f933bcc9efd0473bac3b4aa584a6f7c1c8df8/mypy_extensions-1.1.0-py3-none-any.whl
@@ -212,6 +220,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/b4/f6/1c671874560a70d902dd57028a75411c176910de2df3d6a6a533de424131/cyclopts-4.21.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/ba/1e/acc4d70f88a0a277e4a1fa77ebb985ceabaf900430f875bf9338e11c9420/pydantic_core-2.46.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/c9/87/a51030071ed0e4a9a9a411420d671353a1a5ea834b3e53091e2de44d4e48/genoray-5.0.0-cp310-abi3-manylinux_2_28_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/ca/d0/411c82285a7586e97326020f6b5ecbc2f2ffcbef72aa108c897de1b0a540/pandera-0.32.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/cc/e4/d71e71edc972d534f51cff72fa30edb8b0e5df109b2e5ae67a3985faebb9/joblib_progress-1.0.6-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/ce/7d/0b8e265c43978292425249ae1fd63d5f7b0a719c78eee70055751b5bb8cb/oxbow-0.5.2-cp39-abi3-manylinux_2_28_x86_64.whl
@@ -336,7 +345,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/wrapt-2.1.2-py310h72544b6_0.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/yaml-0.2.5-h925e9cb_3.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.7-hbf9d68e_6.conda
-      - pypi: .
+      - pypi: ./
       - pypi: https://files.pythonhosted.org/packages/08/75/ec73e38812bca7c2240aff481b9ddff20d1ad2f10dee4b3353f5eeaacdab/polars-1.37.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/0c/29/0348de65b8cc732daa3e33e67806420b2ae89bdce2b04af740289c5c6c8c/loguru-0.7.3-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/13/4f/66d99628ff8ce7857aca52fed8f0066ce209f96be2fede6cef9f84e8d04f/pandas-2.3.3-cp310-cp310-macosx_11_0_arm64.whl
@@ -350,7 +359,6 @@ environments:
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-      - pypi: https://files.pythonhosted.org/packages/4b/fe/c6498d404af1089eec01d9a60810223910ea87d5c8015bc5b6986e8f612f/genoray-4.0.1-cp310-abi3-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/55/5e/f8f4f7cc9b24b35103eb9e19f0f69935d16b878b4c5e4511ecd2261403fb/vcfixture-0.6.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/56/c6/65f646c7ff09bd257f660434adb45c4dfcbbcebcc030562fecf6f5bf887d/pydantic_core-2.46.4-cp310-cp310-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/5b/29/74eeb4d3f3ae61ca096b018ad486b3b3c74b17bec09ab4edab721cbefec3/typeguard-4.5.2-py3-none-any.whl
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       - pypi: https://files.pythonhosted.org/packages/0c/29/0348de65b8cc732daa3e33e67806420b2ae89bdce2b04af740289c5c6c8c/loguru-0.7.3-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/0c/2c/d4d96c78e72031f3171fb3a584b557d79d191e9bb4e93747f793c18f8623/fast_histogram-0.14-cp39-abi3-macosx_11_0_arm64.whl
@@ -4873,7 +4882,6 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/2a/2d/d4bf65e47cea8ff2c794a600c4fd1273a7902f268757c531e0ee9f18aa58/pooch-1.9.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/2a/68/1fc93dd759605b5d00fc98b50200739e41ed32bd22d6ba35ca6c3932371b/rich_rst-2.1.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/3b/92/73ab995881de743ddfebe51e6ed35aa6bd709ae7f09eea2cc8e9716bfa36/seqpro-0.22.0-cp39-abi3-macosx_11_0_arm64.whl
-      - pypi: https://files.pythonhosted.org/packages/4b/fe/c6498d404af1089eec01d9a60810223910ea87d5c8015bc5b6986e8f612f/genoray-4.0.1-cp310-abi3-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/55/5e/f8f4f7cc9b24b35103eb9e19f0f69935d16b878b4c5e4511ecd2261403fb/vcfixture-0.6.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/56/c6/65f646c7ff09bd257f660434adb45c4dfcbbcebcc030562fecf6f5bf887d/pydantic_core-2.46.4-cp310-cp310-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/5b/29/74eeb4d3f3ae61ca096b018ad486b3b3c74b17bec09ab4edab721cbefec3/typeguard-4.5.2-py3-none-any.whl
@@ -4900,6 +4908,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/a7/06/3d6badcf13db419e25b07041d9c7b4a2c331d3f4e7134445ec5df57714cd/coloredlogs-15.0.1-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/a7/5f/ed01f9a3cdffbd5a008556fc7b2a08ddb1cc6ace7effa7340604b1d16699/docstring_parser-0.18.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/a9/a6/aa38bddc9f8d90e5ce14023f06ccbf642ab5d507da1ffafb031c0f332dc6/numerary-0.4.4-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/ae/fa/9788f3e8457d419d51a6fa35cb334ebff40e2f8ef5a15a62a776f685e646/genoray-5.0.0-cp310-abi3-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/b2/16/9298cca16e26d2fc3751a2b93469cc14a6f8bb9fb5f4087977926d936383/hirola-0.3.0-py3-none-macosx_10_6_universal2.whl
       - pypi: https://files.pythonhosted.org/packages/b4/f6/1c671874560a70d902dd57028a75411c176910de2df3d6a6a533de424131/cyclopts-4.21.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/c1/39/2c9aea082383c8d41d0d8b8f9907dc6273f8cee47a8c83d0c8bad02488b4/pysam-0.24.0-cp310-cp310-macosx_11_0_arm64.whl
@@ -9863,7 +9872,7 @@ packages:
   license: MIT
   license_family: MIT
   purls:
-  - pkg:pypi/zipp?source=compressed-mapping
+  - pkg:pypi/zipp?source=hash-mapping
   size: 24190
   timestamp: 1779159948016
 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/_openmp_mutex-4.5-7_kmp_llvm.conda
@@ -11603,11 +11612,11 @@ packages:
   purls: []
   size: 433413
   timestamp: 1764777166076
-- pypi: .
+- pypi: ./
   name: genvarloader
   requires_dist:
   - seqpro>=0.22
-  - genoray>=3.4.0,<5
+  - genoray>=5,<6
   - numpy
   - loguru
   - natsort
@@ -13320,41 +13329,6 @@ packages:
   requires_dist:
   - typing-extensions>=4.1.0 ; python_full_version < '3.11'
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/4b/fe/c6498d404af1089eec01d9a60810223910ea87d5c8015bc5b6986e8f612f/genoray-4.0.1-cp310-abi3-macosx_11_0_arm64.whl
-  name: genoray
-  version: 4.0.1
-  sha256: 86f4bada63399c334dcb5e3d496e77b85c58007319a05da2a337d0e76bafbc29
-  requires_dist:
-  - seqpro>=0.21.1,<0.23
-  - numpy>=1.26
-  - pandas>=2.2.3
-  - hirola>=0.3.0
-  - pgenlib>=0.91.0
-  - cyvcf2>=0.31.1
-  - pysam>=0.22
-  - polars>=1.37.1
-  - polars-bio>=0.20.1,<0.34
-  - pyranges>=0.1.3
-  - rich>=13
-  - typing-extensions>=4.14
-  - pyarrow>=21
-  - tqdm>=4.65
-  - phantom-types>=3
-  - more-itertools>=10
-  - loguru>=0.7.0
-  - attrs
-  - awkward
-  - numba
-  - cyclopts
-  - zstandard
-  - pydantic
-  - oxbow>=0.5.1,<0.6
-  - joblib>=1.4.2,<2
-  - joblib-progress>=1.0.6,<2
-  - filelock>3,<4
-  - scipy>=1.10
-  - pooch>=1.7
-  requires_python: '>=3.10,<3.15'
 - pypi: https://files.pythonhosted.org/packages/4d/a1/bca7fd3d452b272e13335db8d6b0b3ecde0f90ad6f16f3328c6fb150c889/rpds_py-0.30.0-cp312-cp312-macosx_11_0_arm64.whl
   name: rpds-py
   version: 0.30.0
@@ -14267,41 +14241,6 @@ packages:
   version: 10.3.7.77
   sha256: a42cd1344297f70b9e39a1e4f467a4e1c10f1da54ff7a85c12197f6c652c8bdf
   requires_python: '>=3'
-- pypi: https://files.pythonhosted.org/packages/73/48/8980acebec96c6615639e44471e00023f15274ce027e485805b0c8b49280/genoray-4.0.1-cp310-abi3-manylinux_2_28_x86_64.whl
-  name: genoray
-  version: 4.0.1
-  sha256: 8f5e25527b0f5489c2dc38e563209c2a4f0819aeb9fa171f5584c1a0e078473d
-  requires_dist:
-  - seqpro>=0.21.1,<0.23
-  - numpy>=1.26
-  - pandas>=2.2.3
-  - hirola>=0.3.0
-  - pgenlib>=0.91.0
-  - cyvcf2>=0.31.1
-  - pysam>=0.22
-  - polars>=1.37.1
-  - polars-bio>=0.20.1,<0.34
-  - pyranges>=0.1.3
-  - rich>=13
-  - typing-extensions>=4.14
-  - pyarrow>=21
-  - tqdm>=4.65
-  - phantom-types>=3
-  - more-itertools>=10
-  - loguru>=0.7.0
-  - attrs
-  - awkward
-  - numba
-  - cyclopts
-  - zstandard
-  - pydantic
-  - oxbow>=0.5.1,<0.6
-  - joblib>=1.4.2,<2
-  - joblib-progress>=1.0.6,<2
-  - filelock>3,<4
-  - scipy>=1.10
-  - pooch>=1.7
-  requires_python: '>=3.10,<3.15'
 - pypi: https://files.pythonhosted.org/packages/73/f7/b1884cb3188ab181fc81fa00c266699dab600f927a964df02ec3d5d1916a/sphinx-9.1.0-py3-none-any.whl
   name: sphinx
   version: 9.1.0
@@ -15658,6 +15597,40 @@ packages:
   - bioframe ; extra == 'viz'
   - matplotlib ; extra == 'viz'
   requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/ae/fa/9788f3e8457d419d51a6fa35cb334ebff40e2f8ef5a15a62a776f685e646/genoray-5.0.0-cp310-abi3-macosx_11_0_arm64.whl
+  name: genoray
+  version: 5.0.0
+  sha256: f5b5f3c4f296ed7e4013db8546c2528f32a520d5f09e36a0c4b3463ce1641258
+  requires_dist:
+  - seqpro>=0.21.1,<0.23
+  - numpy>=1.26
+  - pandas>=2.2.3
+  - hirola>=0.3.0
+  - pgenlib>=0.91.0
+  - cyvcf2>=0.31.1
+  - pysam>=0.22
+  - polars>=1.37.1
+  - polars-bio>=0.20.1,<0.34
+  - rich>=13
+  - typing-extensions>=4.14
+  - pyarrow>=21
+  - tqdm>=4.65
+  - phantom-types>=3
+  - more-itertools>=10
+  - loguru>=0.7.0
+  - attrs
+  - awkward
+  - numba
+  - cyclopts
+  - zstandard
+  - pydantic
+  - oxbow>=0.5.1,<0.6
+  - joblib>=1.4.2,<2
+  - joblib-progress>=1.0.6,<2
+  - filelock>3,<4
+  - scipy>=1.10
+  - pooch>=1.7
+  requires_python: '>=3.10,<3.15'
 - pypi: https://files.pythonhosted.org/packages/af/eb/ff4b8c503fa1f1796679dce648854d58751982426e4e4b37d6fce49d259c/nvidia_cublas_cu12-12.6.4.1-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
   name: nvidia-cublas-cu12
   version: 12.6.4.1
@@ -16262,6 +16235,40 @@ packages:
   version: 3.0.1
   sha256: 6cd7b3897da8d6c9ffb968a6781fa6532dce9c3618a4b127d920dab764a19064
   requires_python: '!=3.0.*,!=3.1.*,!=3.2.*'
+- pypi: https://files.pythonhosted.org/packages/c9/87/a51030071ed0e4a9a9a411420d671353a1a5ea834b3e53091e2de44d4e48/genoray-5.0.0-cp310-abi3-manylinux_2_28_x86_64.whl
+  name: genoray
+  version: 5.0.0
+  sha256: 1acf4a99c9afb196cfe8c9c53ad3e82668d092c6c72626c5ff6777f080afa07e
+  requires_dist:
+  - seqpro>=0.21.1,<0.23
+  - numpy>=1.26
+  - pandas>=2.2.3
+  - hirola>=0.3.0
+  - pgenlib>=0.91.0
+  - cyvcf2>=0.31.1
+  - pysam>=0.22
+  - polars>=1.37.1
+  - polars-bio>=0.20.1,<0.34
+  - rich>=13
+  - typing-extensions>=4.14
+  - pyarrow>=21
+  - tqdm>=4.65
+  - phantom-types>=3
+  - more-itertools>=10
+  - loguru>=0.7.0
+  - attrs
+  - awkward
+  - numba
+  - cyclopts
+  - zstandard
+  - pydantic
+  - oxbow>=0.5.1,<0.6
+  - joblib>=1.4.2,<2
+  - joblib-progress>=1.0.6,<2
+  - filelock>3,<4
+  - scipy>=1.10
+  - pooch>=1.7
+  requires_python: '>=3.10,<3.15'
 - pypi: https://files.pythonhosted.org/packages/ca/d0/411c82285a7586e97326020f6b5ecbc2f2ffcbef72aa108c897de1b0a540/pandera-0.32.1-py3-none-any.whl
   name: pandera
   version: 0.32.1
diff --git a/pixi.toml b/pixi.toml
index f24cabdb..17715a7f 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -102,13 +102,13 @@ numba = "==0.59.1"
 pyarrow = ">=21"
 hirola = "==0.3"
 seqpro = "==0.22.0"
-# genoray >=4.1.0 as the prebuilt abi3 wheel from PyPI — one cp310-abi3 wheel covers
-# py310-313 on both platforms. 4.1.0 carries
+# genoray >=5 as the prebuilt abi3 wheel from PyPI — one cp310-abi3 wheel covers
+# py310-313 on both platforms. 5.0.0 carries
 # SparseVar2._find_ranges_chunked_sparse, the sparse chunked range API
 # _write_from_svar2 consumes (gvl#405), and the keyword-only, struct-grouped
-# _core.run_conversion_pipeline the test fixtures call (d-laub/genoray#153).
+# _core pipeline entry points the test fixtures call (d-laub/genoray#153, #200).
 # Mirrors the pyproject range.
-genoray = ">=4.1.0,<5"
+genoray = ">=5,<6"
 polars = "==1.37.1"
 loguru = "*"
 natsort = "*"
diff --git a/pyproject.toml b/pyproject.toml
index 09b2351e..0a88e632 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,12 +11,13 @@ license = { file = "LICENSE.txt" }
 requires-python = ">=3.10,<3.14" # >= 3.14 blocked by pyarrow/genoray
 dependencies = [
     "seqpro>=0.22",
-    # >=3.4.0 carries SparseVar2._find_ranges_chunked, the memory-bounded chunked
-    # range API _write_from_svar2 consumes to avoid materializing a whole
-    # contig's ranges at once (gvl#333). 4.x is supported: its breaking changes
-    # (SparseVar2.from_vcf(tune=) removal, from_vcf_list(max_mem=) semantics)
-    # are on APIs GVL never calls.
-    "genoray>=4.1.0,<5",
+    # >=5 carries SparseVar2._find_ranges_chunked_sparse, the sparse chunked
+    # range API _write_from_svar2 consumes (gvl#405), and the keyword-only,
+    # struct-grouped _core pipeline entry points the test fixtures call
+    # (d-laub/genoray#153, #200). 5.0.0's breaking changes -- the GENORAY_*
+    # environment variables, SparseVar2.from_vcf(reader_workers=) and
+    # resolve_log_level -- are all on APIs GVL never calls.
+    "genoray>=5,<6",
     "numpy",
     "loguru",
     "natsort",
diff --git a/tests/dataset/test_svar2_contig_naming.py b/tests/dataset/test_svar2_contig_naming.py
index c6beedc9..b6d1ebd7 100644
--- a/tests/dataset/test_svar2_contig_naming.py
+++ b/tests/dataset/test_svar2_contig_naming.py
@@ -40,6 +40,7 @@
 def ensembl_svar2_store(tmp_path_factory) -> Path:
     """A ``.svar2`` store whose only contig is spelled ``1``."""
     from genoray import _core
+    from genoray._pipeline_args import FieldSpec, PlanSettings, RegionSpec
 
     d = tmp_path_factory.mktemp("svar2_contig_naming")
     ref = d / "ref.fa"
@@ -54,15 +55,17 @@ def ensembl_svar2_store(tmp_path_factory) -> Path:
 
     out = d / "store.svar2"
     _core.run_conversion_pipeline(
-        str(bcf),
-        str(ref),
-        ["1"],
-        str(out),
-        ["S0", "S1"],
-        25_000,
-        2,
-        1,
-        8 * 1024 * 1024,
+        vcf_path=str(bcf),
+        reference_path=str(ref),
+        output_dir=str(out),
+        regions=RegionSpec(chroms=["1"], samples=["S0", "S1"]),
+        fields=FieldSpec(),
+        plan=PlanSettings(
+            chunk_size=25_000,
+            max_threads=1,
+            long_allele_capacity=8 * 1024 * 1024,
+        ),
+        ploidy=2,
     )
     assert (out / "meta.json").exists(), "conversion did not finish"
     return out
diff --git a/tests/dataset/test_svar2_dataset.py b/tests/dataset/test_svar2_dataset.py
index b80cbe26..b073046e 100644
--- a/tests/dataset/test_svar2_dataset.py
+++ b/tests/dataset/test_svar2_dataset.py
@@ -112,18 +112,21 @@ def svar_fixture(_src, tmp_path_factory) -> Path:
 def svar2_fixture(_src, tmp_path_factory) -> Path:
     bcf, ref = _src
     from genoray import _core
+    from genoray._pipeline_args import FieldSpec, PlanSettings, RegionSpec
 
     out = tmp_path_factory.mktemp("svar2") / "store.svar2"
     _core.run_conversion_pipeline(
-        str(bcf),
-        str(ref),
-        ["chr1"],
-        str(out),
-        ["S0", "S1"],
-        25_000,
-        2,
-        1,
-        8 * 1024 * 1024,
+        vcf_path=str(bcf),
+        reference_path=str(ref),
+        output_dir=str(out),
+        regions=RegionSpec(chroms=["chr1"], samples=["S0", "S1"]),
+        fields=FieldSpec(),
+        plan=PlanSettings(
+            chunk_size=25_000,
+            max_threads=1,
+            long_allele_capacity=8 * 1024 * 1024,
+        ),
+        ploidy=2,
     )
     assert (out / "meta.json").exists(), "svar2 conversion did not finish"
     return out
@@ -788,18 +791,21 @@ def svar_fixture2(_src2, tmp_path_factory) -> Path:
 def svar2_fixture2(_src2, tmp_path_factory) -> Path:
     bcf, ref = _src2
     from genoray import _core
+    from genoray._pipeline_args import FieldSpec, PlanSettings, RegionSpec
 
     out = tmp_path_factory.mktemp("svar2_mc") / "store.svar2"
     _core.run_conversion_pipeline(
-        str(bcf),
-        str(ref),
-        ["chr1", "chr2"],
-        str(out),
-        ["S0", "S1"],
-        25_000,
-        2,
-        1,
-        8 * 1024 * 1024,
+        vcf_path=str(bcf),
+        reference_path=str(ref),
+        output_dir=str(out),
+        regions=RegionSpec(chroms=["chr1", "chr2"], samples=["S0", "S1"]),
+        fields=FieldSpec(),
+        plan=PlanSettings(
+            chunk_size=25_000,
+            max_threads=1,
+            long_allele_capacity=8 * 1024 * 1024,
+        ),
+        ploidy=2,
     )
     assert (out / "meta.json").exists(), "svar2 conversion did not finish"
     return out