From 03e7ada2ac603c51918a5e671c25107e066fc5cd Mon Sep 17 00:00:00 2001
From: Hanna JULIENNE <hanna.julienne@pasteur.fr>
Date: Mon, 23 Jan 2023 12:54:26 +0100
Subject: [PATCH] specify types when reading regions files to complute ld
matrices
---
raiss/ld_matrix.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/raiss/ld_matrix.py b/raiss/ld_matrix.py
index 982e141..8e33cc0 100644
--- a/raiss/ld_matrix.py
+++ b/raiss/ld_matrix.py
@@ -117,7 +117,7 @@ def generate_genome_matrices(region_files, reffolder, folder_output, prefix, suf
prefix (str): part of file name in reffolder before the chromosome number
suffix (str): part of file name in reffolder after the chromosome number (without extension)
"""
- regions = pd.read_csv(region_files,sep=separa)
+ regions = pd.read_csv(region_files,sep=separa, dtype={'chr':str, 'start':np.int64, 'stop':np.int64})
for reg in regions.iterrows():
# input reference panel file
--
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