From 6425162323e5ee9c513880604381198279fbdae2 Mon Sep 17 00:00:00 2001
From: Cornelius Roemer <cornelius.roemer@gmail.com>
Date: Wed, 17 Apr 2024 18:36:35 +0200
Subject: [PATCH] Add new lineages B.1.21, B.1.22, C.1.1 to phylogenetic

---
 phylogenetic/build-configs/ci/config.yaml |  3 +++
 phylogenetic/defaults/clades.tsv          | 12 ++++++++++++
 phylogenetic/defaults/color_ordering.tsv  |  3 +++
 phylogenetic/defaults/hmpxv1/config.yaml  |  3 +++
 phylogenetic/defaults/mpxv/config.yaml    |  3 +++
 5 files changed, 24 insertions(+)

diff --git a/phylogenetic/build-configs/ci/config.yaml b/phylogenetic/build-configs/ci/config.yaml
index de6d5ed0..31c103c7 100644
--- a/phylogenetic/build-configs/ci/config.yaml
+++ b/phylogenetic/build-configs/ci/config.yaml
@@ -54,7 +54,10 @@ subsample:
       - B.1.18
       - B.1.19
       - B.1.20
+      - B.1.21
+      - B.1.22
       - C.1
+      - C.1.1
   b1:
     group_by: "--group-by country year"
     sequences_per_group: "--subsample-max-sequences 100"
diff --git a/phylogenetic/defaults/clades.tsv b/phylogenetic/defaults/clades.tsv
index 2dbb21be..38674914 100644
--- a/phylogenetic/defaults/clades.tsv
+++ b/phylogenetic/defaults/clades.tsv
@@ -61,6 +61,10 @@ C.1	nuc	55133	A
 C.1	nuc	64426	T
 C.1	nuc	105923	A
 
+C.1.1	clade	C.1
+C.1.1	nuc	21062	T
+C.1.1	nuc	149963	T
+
 B.1.4	clade	B.1
 B.1.4	nuc	34308	A
 
@@ -123,3 +127,11 @@ B.1.20	clade	B.1
 B.1.20	nuc	53326	A
 B.1.20	nuc	164385	T
 B.1.20	nuc	187620	T
+
+B.1.21	clade	B.1
+B.1.21	nuc	22415	A
+B.1.21	nuc	132698	T
+
+B.1.22	clade	B.1
+B.1.22	nuc	34784	T
+B.1.22	nuc	101418	T
diff --git a/phylogenetic/defaults/color_ordering.tsv b/phylogenetic/defaults/color_ordering.tsv
index 7d5871f5..2be351e4 100644
--- a/phylogenetic/defaults/color_ordering.tsv
+++ b/phylogenetic/defaults/color_ordering.tsv
@@ -16904,6 +16904,7 @@ lineage	B.1.1
 lineage	B.1.2
 lineage	B.1.3
 lineage	C.1
+lineage	C.1.1
 lineage	B.1.4
 lineage	B.1.5
 lineage	B.1.6
@@ -16921,6 +16922,8 @@ lineage	B.1.17
 lineage	B.1.18
 lineage	B.1.19
 lineage	B.1.20
+lineage	B.1.21
+lineage	B.1.22
 lineage	A.2
 lineage	A.2.1
 lineage	A.2.2
diff --git a/phylogenetic/defaults/hmpxv1/config.yaml b/phylogenetic/defaults/hmpxv1/config.yaml
index 6e416e95..96d00c97 100644
--- a/phylogenetic/defaults/hmpxv1/config.yaml
+++ b/phylogenetic/defaults/hmpxv1/config.yaml
@@ -51,7 +51,10 @@ subsample:
       - B.1.18
       - B.1.19
       - B.1.20
+      - B.1.21
+      - B.1.22
       - C.1
+      - C.1.1
   b1:
     group_by: "--group-by country year"
     sequences_per_group: "--subsample-max-sequences 100"
diff --git a/phylogenetic/defaults/mpxv/config.yaml b/phylogenetic/defaults/mpxv/config.yaml
index 5327d6f2..30cce340 100644
--- a/phylogenetic/defaults/mpxv/config.yaml
+++ b/phylogenetic/defaults/mpxv/config.yaml
@@ -49,7 +49,10 @@ subsample:
       - B.1.18
       - B.1.19
       - B.1.20
+      - B.1.21
+      - B.1.22
       - C.1
+      - C.1.1
   b1:
     group_by: "--group-by country year"
     sequences_per_group: "--subsample-max-sequences 100"