From 732019dc0d74c989b5aaea1a3b58a9c6ec8cbedb Mon Sep 17 00:00:00 2001
From: ssjunnebo <sara.sjunnebo@scilifelab.se>
Date: Tue, 3 Feb 2026 11:38:36 +0100
Subject: [PATCH 1/4] Set mask to N* if read or index is 0

---
 taca/element/Element_Runs.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/taca/element/Element_Runs.py b/taca/element/Element_Runs.py
index e3c64445..f7aacfb9 100644
--- a/taca/element/Element_Runs.py
+++ b/taca/element/Element_Runs.py
@@ -64,9 +64,9 @@ def get_mask(
     ], f"Mask prefix {prefix} not recognized"
     assert keep in ["bases", "Ns"], f"Keep option {keep} not recognized"
 
-    # Handle no-input cases
+    # Handle no-input cases (e.g. read setups like 144nt(R1)-6nt(I1)-0nt(I2)-0nt(R2))
     if seq == "":
-        mask = f"{prefix}N{cycles_used}"
+        mask = f"{prefix}N*"
         return mask
 
     # Define dict to convert base to mask classifier

From 8abd2a4d4252a3652cd180525c13963d35dd6f1b Mon Sep 17 00:00:00 2001
From: ssjunnebo <sara.sjunnebo@scilifelab.se>
Date: Tue, 3 Feb 2026 14:06:54 +0100
Subject: [PATCH 2/4] Versioning

---
 VERSIONLOG.md    | 4 ++++
 taca/__init__.py | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/VERSIONLOG.md b/VERSIONLOG.md
index 29c618bc..11b32c21 100644
--- a/VERSIONLOG.md
+++ b/VERSIONLOG.md
@@ -1,5 +1,9 @@
 # TACA Version Log
 
+##20260203.1
+
+Set mask to N* if read or index is 0 for AVITI
+
 ##20260127.1
 
 Email when MismatchThreshold is set to 0 for AVITI runs
diff --git a/taca/__init__.py b/taca/__init__.py
index 35d2b951..4a7bd461 100644
--- a/taca/__init__.py
+++ b/taca/__init__.py
@@ -1,3 +1,3 @@
 """Main TACA module"""
 
-__version__ = "1.6.15"
+__version__ = "1.6.16"

From 0fc68ebb13969277adc188fdc7cacb634794af74 Mon Sep 17 00:00:00 2001
From: ssjunnebo <sara.sjunnebo@scilifelab.se>
Date: Tue, 3 Feb 2026 14:08:52 +0100
Subject: [PATCH 3/4] prettier

---
 VERSIONLOG.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/VERSIONLOG.md b/VERSIONLOG.md
index 11b32c21..9023acfd 100644
--- a/VERSIONLOG.md
+++ b/VERSIONLOG.md
@@ -1,18 +1,18 @@
 # TACA Version Log
 
-##20260203.1
+## 20260203.1
 
 Set mask to N* if read or index is 0 for AVITI
 
-##20260127.1
+## 20260127.1
 
 Email when MismatchThreshold is set to 0 for AVITI runs
 
-##20251127.1
+## 20251127.1
 
 Enable archiving of Aviti Teton runs to PDC
 
-##20251121.1
+## 20251121.1
 
 Exclude pod5 from delivery by default
 

From faaa45161ce9087e0504bcf59f50a75764914946 Mon Sep 17 00:00:00 2001
From: ssjunnebo <sara.sjunnebo@scilifelab.se>
Date: Tue, 3 Feb 2026 14:14:27 +0100
Subject: [PATCH 4/4] more prettier

---
 VERSIONLOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VERSIONLOG.md b/VERSIONLOG.md
index 9023acfd..42e8e6fa 100644
--- a/VERSIONLOG.md
+++ b/VERSIONLOG.md
@@ -2,7 +2,7 @@
 
 ## 20260203.1
 
-Set mask to N* if read or index is 0 for AVITI
+Set mask to N\* if read or index is 0 for AVITI
 
 ## 20260127.1