sai-pg 1.0.0__tar.gz → 1.0.1__tar.gz

{sai_pg-1.0.0/sai_pg.egg-info → sai_pg-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sai-pg
-Version: 1.0.0
+Version: 1.0.1
 Summary: A Python Package for Statistics for Adaptive Introgression
 Home-page: https://github.com/xin-huang/sai
 Author: Xin Huang

{sai_pg-1.0.0 → sai_pg-1.0.1}/sai/utils/generators/chunk_generator.py

@@ -131,18 +131,12 @@ class ChunkGenerator(DataGenerator):
         remainder = len(windows) % num_chunks
         result = []
         start_idx = 0
-        prev_end = None
 
         for i in range(num_chunks):
             end_idx = start_idx + avg + (1 if i < remainder else 0)
             sub = windows[start_idx:end_idx]
             if sub:
-                min_start = sub[0][0]
-                max_end = sub[-1][1]
-                if (prev_end is not None) and (min_start < prev_end):
-                    min_start = prev_end + 1
-                result.append((min_start, max_end))
-                prev_end = max_end
+                result.append((sub[0][0], sub[-1][1]))
             start_idx = end_idx
 
         return result

{sai_pg-1.0.0 → sai_pg-1.0.1}/sai/utils/generators/window_generator.py

@@ -125,6 +125,7 @@ class WindowGenerator(DataGenerator):
                 ),
                 window_size=self.win_len,
                 step_size=self.win_step,
+                start=start,
             )
             for tgt_pop in self.tgt_samples
         }
@@ -152,21 +153,21 @@ class WindowGenerator(DataGenerator):
             for start, end in self.tgt_windows[tgt_pop]:
                 ref_gts = self.ref_data[ref_pop].GT[
                     (self.ref_data[ref_pop].POS >= start)
-                    & (self.ref_data[ref_pop].POS < end)
+                    & (self.ref_data[ref_pop].POS <= end)
                 ]
                 tgt_gts = self.tgt_data[tgt_pop].GT[
                     (self.tgt_data[tgt_pop].POS >= start)
-                    & (self.tgt_data[tgt_pop].POS < end)
+                    & (self.tgt_data[tgt_pop].POS <= end)
                 ]
                 src_gts_list = [
                     self.src_data[src_pop].GT[
                         (self.src_data[src_pop].POS >= start)
-                        & (self.src_data[src_pop].POS < end)
+                        & (self.src_data[src_pop].POS <= end)
                     ]
                     for src_pop in src_comb
                 ]
 
-                sub_pos = tgt_pos[(tgt_pos >= start) & (tgt_pos < end)]
+                sub_pos = tgt_pos[(tgt_pos >= start) & (tgt_pos <= end)]
 
                 yield {
                     "chr_name": self.chr_name,

{sai_pg-1.0.0 → sai_pg-1.0.1}/sai/utils/utils.py

@@ -608,6 +608,7 @@ def split_genome(
     pos: np.ndarray,
     window_size: int,
     step_size: int,
+    start: int = None,
 ) -> list[tuple]:
     """
     Creates sliding windows along the genome based on variant positions.
@@ -620,6 +621,9 @@ def split_genome(
         Length of each sliding window.
     step_size : int
         Step size of the sliding windows.
+    start: int, optional
+        Minimum starting coordinate for the first window. The first window will start
+        no smaller than this value. Default is None.
 
     Returns
     -------
@@ -644,7 +648,9 @@ def split_genome(
 
     window_positions = []
     win_start = (pos[0] + step_size) // step_size * step_size - window_size + 1
-    win_start = max(win_start, 1)
+    if start is None:
+        start = 1
+    win_start = max(win_start, start)
 
     # Create windows based on step size and window size
     while win_start <= pos[-1]:

{sai_pg-1.0.0 → sai_pg-1.0.1/sai_pg.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sai-pg
-Version: 1.0.0
+Version: 1.0.1
 Summary: A Python Package for Statistics for Adaptive Introgression
 Home-page: https://github.com/xin-huang/sai
 Author: Xin Huang

{sai_pg-1.0.0 → sai_pg-1.0.1}/setup.py

@@ -32,7 +32,7 @@ with open(os.path.join(HERE, "README.md")) as fid:
 setup(
     name="sai-pg",
     python_requires="==3.9.19",
-    version="1.0.0",
+    version="1.0.1",
     description="A Python Package for Statistics for Adaptive Introgression",
     long_description=README,
     long_description_content_type="text/markdown",