From a4313e2cc0f8548946186838a4ce67e358e46bbe Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 10 Jan 2024 08:00:25 +0300
Subject: Provide convenience functions to avoid subtle call errors

---
 r_qtl/r_qtl2.py                    | 5 +++++
 scripts/rqtl2/install_genotypes.py | 6 +-----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index d8231bb..b2a7acf 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -289,3 +289,8 @@ def validate_bundle(zfile: ZipFile):
             __member_exists_p__(zfile, cdata["cross_info"]["file"])
     except KeyError as kerr:
         raise InvalidFormat(*kerr.args) from kerr
+
+def genotype_data(zfile: ZipFile):
+    """Convenience function to genotype data from R/qtl2 bundle."""
+    cdata = control_data(zfile)
+    return file_data(zfile, "geno", cdata, *make_process_data_geno(cdata))
diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index a555d46..6ae3788 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -132,11 +132,7 @@ def install_genotypes(dbconn: mdb.Connection,
             logger.info(("Loading genotypes. This could take a while. "
                          "Please be patient."))
 
-            cdata = rqtl2.control_data(zfile)
-            genotypes = rqtl2.file_data(zfile,
-                                        "geno",
-                                        cdata,
-                                        rqtl2.make_process_data_geno(cdata))
+            genotypes = rqtl2.genotype_data(zfile)
             while True:
                 batch = tuple(take(genotypes, 5000))
                 if len(batch) == 0:
-- 
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