resources: add proposed lineages for #197 #198 #199

ktmeaton · Nov 7, 2022 · 375c3a7 · 375c3a7
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diff --git a/.github/ISSUE_TEMPLATE/lineage-validation.md b/.github/ISSUE_TEMPLATE/lineage-validation.md
@@ -1,4 +1,5 @@
-[pango-designation issue XXX](https://github.com/cov-lineages/pango-designation/issues/XXX)
+- pango-designation issue: [# XXX](https://github.com/cov-lineages/pango-designation/issues/XXX)
+- covSPECTRUM query:
 
 ## Parents
 

diff --git a/defaults/parameters.yaml b/defaults/parameters.yaml
@@ -82,7 +82,7 @@ rule_params:
       - delta_omicron:   "--clades 21I 21J BA.1 BA.2           --ansi --parents 2-4 --breakpoints 0-10 --unique 1 --max-ambiguous 20 --max-intermission-length 2 --max-intermission-count 3  --ignore-shared --mutation-threshold 0.25"
       - omicron_omicron: "--clades BA.1 BA.2 BA.4 BA.5         --ansi --parents 2-4 --breakpoints 0-10 --unique 1 --max-ambiguous 20 --max-intermission-length 2 --max-intermission-count 3  --ignore-shared --mutation-threshold 0.25"
       # Current Variants of Concern and Dominant Lineages
-      - voc:             "--clades BA.2.10 BA.2.3.20 BA.2.75 BA.4.6 BA.5.2 BA.5.3 XBB --ansi --parents 2-4 --breakpoints 1-5 --unique 1 --max-ambiguous 20 --max-intermission-length 2 --max-intermission-count 3  --ignore-shared --mutation-threshold 0.25"
+      - voc:             "--clades BA.2.10 BA.2.3.17 BA.2.3.20 BA.2.75 BA.4.6 BA.5.2 BA.5.3 XBB --ansi --parents 2-4 --breakpoints 1-5 --unique 1 --max-ambiguous 20 --max-intermission-length 2 --max-intermission-count 3  --ignore-shared --mutation-threshold 0.25"
 
   # ---------------------------------------------------------------------------
   # min_len            : (optional) Ignore recombinant regions shorter than this

diff --git a/resources/breakpoints.tsv b/resources/breakpoints.tsv
@@ -75,5 +75,8 @@ XBC	1100	2791:4183,22579:22673,25470:25583	Omicron/BA.2/21L,Delta/21I,Omicron/BA
 proposed1138	1138	NA	NA
 proposed1139	1139	12161:22791	Omicron/BA.2/21L,Omicron/BA.5/22B
 XBD	1137	23020:25415	Omicron/BA.2.75/22D,Omicron/BA.5/22B
+proposed1229	1229	15452:22000	BA.2.3.17,Omicron/BA.2.75/22D
 XBE	1246	16936:27011	Omicron/BA.5.2,Omicron/BA.5.3
 XBF	1259	5184:9865	Omicron/BA.5/22B,Omicron/BA.2.75/22D
+proposed1296	1296	5184:12443	Omicron/BA.2.75/22D,Omicron/XBB/22F
+proposed1268	1268	23019:23039	Omicron/BA.2/21L,Omicron/BA.5/22B
diff --git a/resources/breakpoints_clade.png b/resources/breakpoints_clade.png