Bug fix in LDMatrix.load.

shz9 · May 22, 2024 · 9cdc274 · 9cdc274
1 parent 987770b
commit 9cdc274
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/magenpy/GWADataLoader.py b/magenpy/GWADataLoader.py
@@ -539,13 +539,13 @@ def read_summary_statistics(self,
             return
 
         if self.verbose and len(sumstats_files) < 2:
-            print("> Reading summary statistics file...")
+            print("> Reading summary statistics...")
 
         self.sumstats_table = {}
 
         for f in tqdm(sumstats_files,
                       total=len(sumstats_files),
-                      desc="Reading summary statistics files",
+                      desc="Reading summary statistics",
                       disable=not self.verbose or len(sumstats_files) < 2):
 
             ss_tab = SumstatsTable.from_file(f, sumstats_format=sumstats_format, parser=parser, **parse_kwargs)
@@ -585,13 +585,13 @@ def read_ld(self, ld_store_paths):
             return
 
         if self.verbose and len(ld_store_files) < 2:
-            print("> Reading LD matrix...")
+            print("> Reading LD metadata...")
 
         self.ld = {}
 
         for f in tqdm(ld_store_files,
                       total=len(ld_store_files),
-                      desc="Reading LD matrices",
+                      desc="Reading LD metadata",
                       disable=not self.verbose or len(ld_store_files) < 2):
             z = LDMatrix.from_path(f)
             self.ld[z.chromosome] = z

diff --git a/magenpy/LDMatrix.py b/magenpy/LDMatrix.py
@@ -1395,7 +1395,8 @@ def load(self,
         self.release()
 
         self._mat = self.load_data(return_symmetric=return_symmetric,
-                                   dtype=dtype)
+                                   dtype=dtype,
+                                   return_as_csr=True)
 
         # Update the flags:
         self.in_memory = True