From a046a45ccae5291a79b339277a59315306b5ff99 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alex=20H=C3=BCbner?= <alexhbnr@gmail.com>
Date: Fri, 7 Feb 2025 16:27:28 +0100
Subject: [PATCH 1/2] Replace algorithm to determine the colour chemistry

It was simplified to when the instrument is not a known Illumina
sequencer with two-dye chemistry, a colour chemistry of four dyes is
assumed.
---
 amdirt/core/__init__.py | 31 ++++++++++++++++++-------------
 1 file changed, 18 insertions(+), 13 deletions(-)

diff --git a/amdirt/core/__init__.py b/amdirt/core/__init__.py
index 634bbc9..616e263 100644
--- a/amdirt/core/__init__.py
+++ b/amdirt/core/__init__.py
@@ -103,24 +103,29 @@ def check_allowed_values(ref: list, test: str):
 
 def get_colour_chemistry(instrument: str) -> int:
     """
-    Get number of colours used in sequencing chemistry
+    Get number of colours used in sequencing chemistry. If the instrument is
+    not a known Illumina sequencer with two-dye chemistry, a colour chemistry
+    of four dyes is assumed. 
+
     Args:
         instrument(str): Name of the instrument
     Returns:
         int: number of colours used in sequencing chemistry
     """
-    chemistry_colours = {
-        "bgiseq": 4,
-        "miseq": 4,
-        "hiseq": 4,
-        "genome analyzer": 4,
-        "nextseq": 2,
-        "novaseq": 2,
-    }
-
-    for k in chemistry_colours:
-        if k in instrument.lower():
-            return chemistry_colours[k]
+    instruments_2dye = [
+        "Illumina MiniSeq",
+        "Illumina NovaSeq 6000",
+        "Illumina NovaSeq X",
+        "Illumina iSeq 100",
+        "NextSeq 1000",
+        "NextSeq 2000",
+        "NextSeq 500",
+        "NextSeq 550",
+    ]
+    if instrument in instruments_2dye:
+        return 2
+    else:
+        return 4
 
 
 def doi2bib(doi: str) -> str:

From c47d7da52df3a4390b84dcb5626771087cb7c136 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alex=20H=C3=BCbner?= <alexhbnr@gmail.com>
Date: Sun, 9 Feb 2025 14:06:41 +0100
Subject: [PATCH 2/2] Update colour chemistry test

---
 tests/test_core.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_core.py b/tests/test_core.py
index 942f3cf..232cfe3 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -7,8 +7,8 @@
 
 def test_get_colour_chemistry():
 
-    assert get_colour_chemistry("hiseq") == 4
-    assert get_colour_chemistry("novaseq") == 2
+    assert get_colour_chemistry("Illumina HiSeq 2500") == 4
+    assert get_colour_chemistry("Illumina NovaSeq 6000") == 2
 
 
 def test_doi2bib():