Bgen to zarr (v2)

requirements.txt

@@ -5,5 +5,6 @@ numpy
 scipy
 xarray
 zarr
-bgen_reader>=4.0.5
+bgen_reader==4.0.5
+git+https://github.com/pangeo-data/rechunker
 git+https://github.com/pystatgen/sgkit

setup.cfg

@@ -54,7 +54,7 @@ ignore =
 [isort]
 default_section = THIRDPARTY
 known_first_party = sgkit
-known_third_party = bgen_reader,dask,numpy,pytest,setuptools,xarray
+known_third_party = bgen_reader,dask,numpy,pytest,rechunker,setuptools,xarray,zarr
 multi_line_output = 3
 include_trailing_comma = True
 force_grid_wrap = 0
@@ -67,9 +67,16 @@ ignore_missing_imports = True
 ignore_missing_imports = True
 [mypy-setuptools.*]
 ignore_missing_imports = True
+[mypy-rechunker.*]
+ignore_missing_imports = True
 [mypy-bgen_reader.*]
 ignore_missing_imports = True
 [mypy-sgkit.*]
 ignore_missing_imports = True
+[mypy-zarr.*]
+ignore_missing_imports = True
 [mypy-sgkit_bgen.tests.*]
 disallow_untyped_defs = False
+[mypy-sgkit_bgen.*]
+allow_redefinition = True
+warn_unused_ignores = False

sgkit_bgen/__init__.py

@@ -1,3 +1,3 @@
-from .bgen_reader import read_bgen  # noqa: F401
+from .bgen_reader import bgen_to_zarr, read_bgen, rechunk_bgen  # noqa: F401
 
-__all__ = ["read_bgen"]
+__all__ = ["read_bgen", "rechunk_bgen", "bgen_to_zarr"]