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"polars>=1.30", + "polars>=1.37.1", "cyvcf2", "pandera", "pysam", @@ -31,7 +31,7 @@ dependencies = [ "awkward", "hirola>=0.3,<0.4", "seqpro>=0.9", - "genoray>=1.0.1,<2", + "genoray>=2.1.1,<3", ] [project.urls] diff --git a/python/genvarloader/_dataset/_rag_variants.py b/python/genvarloader/_dataset/_rag_variants.py index 15e8102..c28ffdf 100644 --- a/python/genvarloader/_dataset/_rag_variants.py +++ b/python/genvarloader/_dataset/_rag_variants.py @@ -15,7 +15,7 @@ ) from genoray._types import DOSAGE_TYPE, POS_TYPE, V_IDX_TYPE from numpy.typing import NDArray -from seqpro.rag import OFFSET_TYPE, Ragged, lengths_to_offsets +from seqpro.rag import OFFSET_TYPE, Ragged, is_rag_dtype, lengths_to_offsets from typing_extensions import Self from .._ragged import reverse_complement @@ -32,8 +32,9 @@ class RaggedVariant(ak.Record): class RaggedVariants(ak.Array): - """An awkward record array, typically with shape (batch, ploidy, ~variants). - Guaranteed to at least have the field "alt" and "start" and one of "ref" or "ilen".""" + """An awkward record array with shape :code:`(batch, ploidy, ~variants, [~length])`. + Guaranteed to at least have the field :code:`"alt"` and :code:`"start"` and one of :code:`"ref"` or :code:`"ilen"`. + """ def __init__( self, @@ -179,8 +180,8 @@ def infer_germline_ccfs_( raise ValueError(f"Cannot infer germline CCFs without {ccf_field}.") ccfs = self[ccf_field] - if not isinstance(ccfs, Ragged): - raise ValueError(f"{ccf_field} must be a Ragged array.") + if not isinstance(ccfs, Ragged) or not is_rag_dtype(ccfs, DOSAGE_TYPE): + raise ValueError(f"{ccf_field} must be a Ragged array of {DOSAGE_TYPE}.") _infer_germline_ccfs( ccfs.data, diff --git a/python/genvarloader/_dataset/_reconstruct.py b/python/genvarloader/_dataset/_reconstruct.py index 4facf1c..ce86c5f 100644 --- a/python/genvarloader/_dataset/_reconstruct.py +++ b/python/genvarloader/_dataset/_reconstruct.py @@ -16,6 +16,7 @@ from einops import repeat from genoray._svar import SparseDosages, SparseGenotypes from genoray._types import DOSAGE_TYPE, POS_TYPE, V_IDX_TYPE +from genoray.exprs import ILEN from loguru import logger from numpy.typing import NDArray from packaging.version import Version @@ -67,6 +68,13 @@ def from_table(cls, path: str | Path, one_based: bool = True): """ path = Path(path).resolve() variants = pl.read_ipc(path, memory_map=False) + if variants.schema["ALT"] == pl.List(pl.Utf8): + ilen = ILEN + else: + ilen = pl.col("ALT").str.len_bytes().cast(pl.Int32) - pl.col( + "REF" + ).str.len_bytes().cast(pl.Int32) + variants = variants.with_columns(ILEN=ilen) is_list_type = [ col for col in ("ALT", "ILEN") if variants[col].dtype == pl.List ] diff --git a/python/genvarloader/_dataset/_write.py b/python/genvarloader/_dataset/_write.py index 405e9ae..e3a1d33 100644 --- a/python/genvarloader/_dataset/_write.py +++ b/python/genvarloader/_dataset/_write.py @@ -248,18 +248,18 @@ def _write_from_vcf(path: Path, bed: pl.DataFrame, vcf: VCF, max_mem: int): if vcf._index is None: if not vcf._valid_index(): logger.info("VCF genoray index is invalid, writing") - vcf._write_gvi_index(progress=True) + vcf._write_gvi_index() vcf._load_index() assert vcf._index is not None - if vcf._index.df.select((pl.col("ALT").list.len() > 1).any()).item(): + if vcf._index.select((pl.col("ALT").list.len() > 1).any()).item(): raise ValueError( "VCF with filtering applied still contains multi-allelic variants. Please filter or split them." ) - shutil.copy(vcf._index_path(), out_dir / "variants.arrow") + (out_dir / "variants.arrow").hardlink_to(vcf._index_path()) unextended_var_idxs: dict[str, list[NDArray[V_IDX_TYPE]]] = {} for (contig,), df in bed.partition_by( @@ -368,7 +368,7 @@ def _write_from_pgen(path: Path, bed: pl.DataFrame, pgen: PGEN, max_mem: int): out_dir = path / "genotypes" out_dir.mkdir(parents=True, exist_ok=True) - shutil.copy(pgen._index_path(), out_dir / "variants.arrow") + (out_dir / "variants.arrow").hardlink_to(pgen._index_path()) pbar = tqdm(total=bed.height, unit=" region") @@ -459,7 +459,7 @@ def _write_from_svar( with open(out_dir / "svar_meta.json", "w") as f: json.dump({"shape": offsets.shape, "dtype": offsets.dtype.str}, f) - v_ends = svar.var_table.select( + v_ends = svar.index.select( end=pl.col("POS") - pl.col("ILEN").list.first().clip(upper_bound=0) )["end"].to_numpy() max_ends = np.empty(bed.height, np.int32) From 77746f9a55e149bc57df1b7f565cc6b209d646c9 Mon Sep 17 00:00:00 2001 From: d-laub Date: Wed, 4 Feb 2026 18:21:47 -0800 Subject: [PATCH 2/5] ci: switch to prek --- pixi.lock | 388 ++++++++++++++++-------------------------------------- pixi.toml | 4 +- 2 files changed, 113 insertions(+), 279 deletions(-) diff --git a/pixi.lock b/pixi.lock index ff7c267..ecfaa26 100644 --- a/pixi.lock +++ b/pixi.lock @@ -35,20 +35,15 @@ environments: - 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depends: - - distlib >=0.3.7,<1 - - filelock >=3.12.2,<4 - - platformdirs >=3.9.1,<5 - - python >=3.10 - - typing_extensions >=4.13.2 - license: MIT - license_family: MIT - purls: - - pkg:pypi/virtualenv?source=hash-mapping - size: 4401341 - timestamp: 1761726489722 - conda: https://conda.anaconda.org/conda-forge/linux-64/watchfiles-1.1.1-py312h0ccc70a_0.conda sha256: 5cc839dafe34e5f7b612e1d4d97bb11546eae8b1842e5b7870b3c6adbe9097e8 md5: d8ecac58c1cb180296a1dd7de058dbc5 diff --git a/pixi.toml b/pixi.toml index d6379f1..97c8688 100644 --- a/pixi.toml +++ b/pixi.toml @@ -23,7 +23,7 @@ samtools = "*" bcftools = "*" plink2 = "*" ruff = "*" -pre-commit = "*" +prek = "*" commitizen = "*" pyarrow = "<22" maturin = ">=1.6,<2" @@ -97,7 +97,7 @@ python = "3.11.*" python = "3.12.*" [tasks] -pre-commit = "pre-commit install --hook-type commit-msg --hook-type pre-push" +prek-install = "prek install --hook-type commit-msg --hook-type pre-push" gen = { cmd = "python tests/data/generate_ground_truth.py" } test = { cmd = "pytest tests && cargo test --release", depends-on = ["gen"] } From 5990acd568431027da078919edb031f2640bbb17 Mon Sep 17 00:00:00 2001 From: d-laub Date: Wed, 4 Feb 2026 18:23:03 -0800 Subject: [PATCH 3/5] ci: prek cmd --- pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.toml b/pixi.toml index 97c8688..cbbca57 100644 --- a/pixi.toml +++ b/pixi.toml @@ -97,7 +97,7 @@ python = "3.11.*" python = "3.12.*" [tasks] -prek-install = "prek install --hook-type commit-msg --hook-type pre-push" +prek-i = "prek install --hook-type commit-msg --hook-type pre-push" gen = { cmd = "python tests/data/generate_ground_truth.py" } test = { cmd = "pytest tests && cargo test --release", depends-on = ["gen"] } From f1e226b8ee788ac4bf59b5eb9c5f8ecb420f8e3a Mon Sep 17 00:00:00 2001 From: d-laub Date: Wed, 4 Feb 2026 18:23:30 -0800 Subject: [PATCH 4/5] ci: prek cfg --- pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.toml b/pixi.toml index cbbca57..97c8688 100644 --- a/pixi.toml +++ b/pixi.toml @@ -97,7 +97,7 @@ python = "3.11.*" python = "3.12.*" [tasks] -prek-i = "prek install --hook-type commit-msg --hook-type pre-push" +prek-install = "prek install --hook-type commit-msg --hook-type pre-push" gen = { cmd = "python tests/data/generate_ground_truth.py" } test = { cmd = "pytest tests && cargo test --release", depends-on = ["gen"] } From 3eeb43f75645ea2df2e18ba983ff4f1d6c9eccd9 Mon Sep 17 00:00:00 2001 From: d-laub Date: Wed, 4 Feb 2026 18:24:42 -0800 Subject: [PATCH 5/5] ci: test workflow --- .github/workflows/test.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 0e0db7c..25aa421 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -22,7 +22,6 @@ jobs: uses: prefix-dev/setup-pixi@v0.9.3 with: pixi-version: v0.62.1 - cache: true environments: ${{ matrix.environment }} - name: Test run: pixi run -e ${{ matrix.environment }} test