From 6462099372626e11706219a695e8303250359510 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 21 Feb 2024 09:19:24 +0300
Subject: Pass 'filename' value to error checker function.

---
 scripts/qc_on_rqtl2_bundle.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

(limited to 'scripts')

diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py
index 027f387..37b8a9e 100644
--- a/scripts/qc_on_rqtl2_bundle.py
+++ b/scripts/qc_on_rqtl2_bundle.py
@@ -97,7 +97,7 @@ def retrieve_errors_with_progress(rconn: Redis,#pylint: disable=[too-many-locals
                     continue
                 if value is not None:
                     for checker in checkers:
-                        error = checker(lineno, field, value)
+                        error = checker(lineno=lineno, field=field, value=value)
                         if bool(error):
                             yield error
                         __update_processed__(value)
@@ -133,9 +133,10 @@ def qc_pheno_errors(rconn, fqjobid, zfile, logger) -> bool:
     cdata = rqtl2.control_data(zfile)
     if "pheno" in cdata:
         logger.info("Checking for errors in the 'pheno' file…")
-        perrs = tuple(retrieve_errors_with_progress(
-            rconn,fqjobid, zfile, "pheno",
-            (partial(decimal_points_error, mini=3),)))
+        perrs = check_pheno_samples(zfile.filename, logger) + tuple(
+            retrieve_errors_with_progress(
+                rconn,fqjobid, zfile, "pheno",
+                (partial(decimal_points_error, filename="pheno", mini=3),)))
         add_to_errors(rconn, fqjobid, "errors-generic", tuple(
             err for err in perrs if isinstance(err, rqfe.MissingFile)))
         add_to_errors(rconn, fqjobid, "errors-pheno", tuple(
-- 
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