From 1bc30149be88a99014ba49fe8738f5668f3a463e Mon Sep 17 00:00:00 2001
From: taranewman <69013600+taranewman@users.noreply.github.com>
Date: Fri, 30 Aug 2024 09:36:43 -0700
Subject: [PATCH] Make Ct 0 for positive control samples (#20)

* Make ct zero for positive control

* fix containerid

* Add ct 0 when library id starts with POS

* remove added whitespace

* fix whitespace
---
 auto_ncov/metadata.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/auto_ncov/metadata.py b/auto_ncov/metadata.py
index 5eec962..283131f 100644
--- a/auto_ncov/metadata.py
+++ b/auto_ncov/metadata.py
@@ -82,7 +82,7 @@ def combine_ct_values(metadata: dict[str, dict[str, object]]) -> dict[str, dict[
             if sample_metadata[ct_field] is not None:
                 ct_combo = sample_metadata[ct_field]
                 break
-
+                
         sample_metadata['ct_combo'] = ct_combo
 
     return metadata
@@ -143,6 +143,9 @@ def select_run_metadata(all_metadata: dict[str, dict[str, object]], run_library_
                 except KeyError as e:
                     pass
 
+        if library_id.startswith('POS'):
+            library_selected_metadata['ct'] = 0
+            
         run_metadata.append(library_selected_metadata)
 
     return run_metadata