using read_cloud_i8 for read_i8 and all tests passed.

fastlmm · Dec 25, 2023 · 7125834 · 7125834
1 parent 99b0baa
commit 7125834
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Showing 8 changed files with 2,488 additions and 2,430 deletions.
diff --git a/bed_reader/__init__.py b/bed_reader/__init__.py
@@ -8,7 +8,7 @@
 from bed_reader._open_bed import get_num_threads, open_bed
 from bed_reader._sample_data import sample_file, tmp_path
 from bed_reader._to_bed import to_bed
-from bed_reader._open_bed_cloud import open_bed_cloud
+# cmk from bed_reader._open_bed_cloud import open_bed_cloud
 
 from .bed_reader import (
     file_aat_piece_f32_orderf,
@@ -20,7 +20,7 @@
     read_f32,
     read_f64,
     read_i8,
-    # cmk read_cloud_i8,
+    read_cloud_i8,
     standardize_f32,
     standardize_f64,
     subset_f32_f32,

diff --git a/bed_reader/_open_bed.py b/bed_reader/_open_bed.py
@@ -13,7 +13,7 @@
 except ImportError:
     sparse = None
 
-from .bed_reader import read_f32, read_f64, read_i8  # type: ignore
+from .bed_reader import read_f32, read_f64, read_i8, read_cloud_i8  # type: ignore
 
 
 # https://stackoverflow.com/questions/845058/how-to-get-line-count-of-a-large-file-cheaply-in-python
@@ -390,7 +390,8 @@ def read(
 
             if self.iid_count > 0 and self.sid_count > 0:
                 if dtype == np.int8:
-                    reader = read_i8
+                    # cmk000
+                    reader = read_cloud_i8
                 elif dtype == np.float64:
                     reader = read_f64
                 elif dtype == np.float32:
@@ -402,7 +403,8 @@ def read(
                     )
 
                 reader(
-                    str(self.filepath),
+                    # cmk000
+                    str(self.filepath.as_posix()),
                     iid_count=self.iid_count,
                     sid_count=self.sid_count,
                     is_a1_counted=self.count_A1,