Merge pull request #57 from cov-lineages/dev

Dev
cov-lineages · Feb 8, 2022 · 584cf29 · 584cf29
2 parents b2fb8e3 + 3784497
commit 584cf29
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Showing 5 changed files with 20 additions and 16 deletions.
diff --git a/constellations/__init__.py b/constellations/__init__.py
@@ -1,3 +1,3 @@
 _program = "constellations"
-__version__ = "v0.1.2"
+__version__ = "v0.1.3"
 
diff --git a/constellations/definitions/cB.1.1.529.json b/constellations/definitions/cB.1.1.529.json
@@ -23,7 +23,6 @@
         "orf1ab:T3255I",
         "orf1ab:P3395H",
         "orf1ab:SGF3675-",
-        "nuc:T13195C",
         "orf1ab:P4715L",
         "orf1ab:I5967V",
         "spike:G142D",
@@ -47,8 +46,6 @@
         "spike:D796Y",
         "spike:Q954H",
         "spike:N969K",
-        "nuc:C25000T",
-        "nuc:C25584T",
         "e:T9I",
         "m:Q19E",
         "m:A63T",
@@ -62,12 +59,12 @@
     "note": "Common mutations to the sublineages found",
     "rules": {
       "default": {
-        "min_alt": 25,
+        "min_alt": 22,
         "max_ref": 5,
         "spike:D614G": "not ref"
       },
       "Probable": {
-        "min_alt": 15,
+        "min_alt": 12,
         "max_ref": 14
       }
     }

diff --git a/constellations/definitions/cBA.1.json b/constellations/definitions/cBA.1.json
@@ -19,10 +19,12 @@
     ],
     "sites": [
         "orf1ab:K856R",
-        "del:6513:3",
         "nuc:T5386G",
+        "del:6513:3",
         "orf1ab:A2710T",
+        "orf1ab:L3674F",
         "orf1ab:I3758V",
+        "nuc:T13195C",
         "nuc:C15240T",
         "spike:A67V",
         "del:21765:6",
@@ -36,20 +38,22 @@
         "spike:T547K",
         "spike:N856K",
         "spike:L981F",
+        "nuc:C25000T",
+        "nuc:C25584T",
         "m:D3G"
     ],
     "note": "Unique mutations for sublineage",
     "note2": "Requires ancestral mutation so scorpio tie breaks correctly",
     "rules": {
       "default": {
-        "min_alt": 10,
+        "min_alt": 14,
         "max_ref": 3,
-        "spike:D614G": "not ref"
+        "nuc:T5386G": "not ref"
       },
       "Probable": {
-        "min_alt": 6,
+        "min_alt": 10,
         "max_ref": 8,
-        "spike:D614G": "not ref"
+        "nuc:T5386G": "not ref"
       }
     }
 }
diff --git a/constellations/definitions/cBA.2.json b/constellations/definitions/cBA.2.json
@@ -30,6 +30,7 @@
         "nuc:G10447A",
         "nuc:C15714T",
         "nuc:C12880T",
+        "nuc:C15714T",
         "orf1ab:R5716C",
         "orf1ab:T6564I",
         "nuc:A20055G",
@@ -40,6 +41,8 @@
         "spike:T376A",
         "spike:D405N",
         "spike:R408S",
+        "nuc:C25000T",
+        "nuc:C25584T",
         "nuc:C26060T",
         "nuc:C26858T",
         "orf6:D61L",
@@ -48,14 +51,14 @@
     "note": "Unique mutations for sublineage",
     "rules": {
       "default": {
-        "min_alt": 16,
+        "min_alt": 18,
         "max_ref": 3,
-        "spike:D614G": "not ref"
+        "nuc:C10198T": "not ref"
       },
       "Probable": {
-        "min_alt": 10,
+        "min_alt": 12,
         "max_ref": 8,
-        "spike:D614G": "not ref"
+        "nuc:C10198T": "not ref"
       }
     }
 }
diff --git a/constellations/definitions/cC.37.json b/constellations/definitions/cC.37.json
@@ -38,7 +38,7 @@
 		"N:G214C"
     ],
     "rules": {
-        "min_alt": 5,
+        "min_alt": 9,
         "max_ref": 3
     }
 }