adjusting definition rules

cov-lineages · Jun 3, 2021 · 7501de4 · 7501de4
1 parent f64737f
commit 7501de4
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Showing 18 changed files with 64 additions and 32 deletions.
diff --git a/constellations/definitions/cA.23.1+E484K.json b/constellations/definitions/cA.23.1+E484K.json
@@ -34,7 +34,7 @@
     ],
     "rules": {
         "min_alt": 5,
-        "max_ref": 13,
+        "max_ref": 3,
         "S:E484K": "alt"
     }
 }
diff --git a/constellations/definitions/cA.23.1.json b/constellations/definitions/cA.23.1.json
@@ -30,6 +30,6 @@
     ],
     "rules": {
         "min_alt": 5,
-        "max_ref": 13
+        "max_ref": 3
     }
 }
diff --git a/constellations/definitions/cAV1.json b/constellations/definitions/cAV1.json
@@ -32,7 +32,7 @@
 		"N:G204R"
 	],
 	"rules": {
-		"min_alt": 6,
-		"max_ref": 0
+		"min_alt": 7,
+		"max_ref": 3
 	}
 }
diff --git a/constellations/definitions/cB.1.1.318.json b/constellations/definitions/cB.1.1.318.json
@@ -39,7 +39,7 @@
         "del:28895:3"
     ],
     "rules": {
-        "min_alt": 5,
-        "max_ref": 19
+        "min_alt": 11,
+        "max_ref": 3
     }
 }
diff --git a/constellations/definitions/cB.1.1.7+E484K.json b/constellations/definitions/cB.1.1.7+E484K.json
@@ -42,8 +42,8 @@
 		"N:S235F"
     ],
     "rules": {
-        "min_alt": 5,
-        "max_ref": 4,
+        "min_alt": 15,
+        "max_ref": 3,
         "S:E484K": "alt"
     }
 }
diff --git a/constellations/definitions/cB.1.1.7.json b/constellations/definitions/cB.1.1.7.json
@@ -43,7 +43,7 @@
 		"N:S235F"
 	],
 	"rules": {
-		"min_alt": 4,
-		"max_ref": 6
+		"min_alt": 15,
+		"max_ref": 3
 	}
 }
diff --git a/constellations/definitions/cB.1.324.1.json b/constellations/definitions/cB.1.324.1.json
@@ -29,7 +29,7 @@
         "nuc:A28272T"
     ],
     "rules": {
-        "min_alt": 8,
-        "max_ref": 9
+        "min_alt": 5,
+        "max_ref": 3
     }
 }
diff --git a/constellations/definitions/cB.1.351.json b/constellations/definitions/cB.1.351.json
@@ -39,7 +39,7 @@
         "del:11287:9"
     ],
     "rules": {
-        "min_alt": 4,
-        "max_ref": 14
+        "min_alt": 6,
+        "max_ref": 3
     }
 }
diff --git a/constellations/definitions/cB.1.427_429.json b/constellations/definitions/cB.1.427_429.json
@@ -19,9 +19,21 @@
         "Eta"
     ],
     "sites": [
+    	"S:S13I",
+		"S:W152C",
+		"S:L452R",
+		"S:D614G",
+		"ORF1a:I4205V",
+		"ORF1b:D1183Y",
+		"nuc:C2395T",
+		"nuc:T2597C",
+		"nuc:T24349C",
+		"nuc:G27890T",
+		"nuc:A28272T"
     ],
     "rules": {
         "min_alt": 5,
-        "max_ref": 16
+        "max_ref": 3
     }
-}
+}
+
diff --git a/constellations/definitions/cB.1.525.json b/constellations/definitions/cB.1.525.json
@@ -40,7 +40,7 @@
         "nuc:G29543T"
     ],
     "rules": {
-        "min_alt": 5,
-        "max_ref": 16
+        "min_alt": 8,
+        "max_ref": 3
     }
 }
diff --git a/constellations/definitions/cB.1.526.json b/constellations/definitions/cB.1.526.json
@@ -17,9 +17,29 @@
         "Eta"
     ],
     "sites": [
+        "nuc:C3037T",
+		"ORF1a:T265I",
+		"ORF1a:L3201P",
+		"1ab:SGF3675-",
+		"ORF1b:P314L",
+		"ORF1b:Q1011H",
+        "nuc:A20262G",
+        "S:L5F",
+		"S:T95I",
+		"S:D253G",
+		"S:E484K",
+		"S:D614G",
+		"S:A701V",
+		"ORF3a:P42L",
+		"ORF3a:Q57H",
+		"N:P199L",
+		"N:M234I",
+		"ORF8:T11I",
+        "nuc:A28271-"
     ],
     "rules": {
-        "min_alt": 5,
-        "max_ref": 16
+        "min_alt": 11,
+        "max_ref": 3
     }
-}
+}
+
diff --git a/constellations/definitions/cB.1.617.1.json b/constellations/definitions/cB.1.617.1.json
@@ -32,6 +32,6 @@
     ],
     "rules": {
         "min_alt": 5,
-        "max_ref": 11
+        "max_ref": 3
     }
 }
diff --git a/constellations/definitions/cB.1.617.2+K417N.json b/constellations/definitions/cB.1.617.2+K417N.json
@@ -34,7 +34,7 @@
     ],
     "rules": {
         "min_alt": 5,
-        "max_ref": 12,
+        "max_ref": 3,
         "S:K417N": "alt"
     }
 }
diff --git a/constellations/definitions/cB.1.617.2.json b/constellations/definitions/cB.1.617.2.json
@@ -35,6 +35,6 @@
     ],
     "rules": {
         "min_alt": 5,
-        "max_ref": 12
+        "max_ref": 3
     }
 }
diff --git a/constellations/definitions/cB.1.617.3.json b/constellations/definitions/cB.1.617.3.json
@@ -36,7 +36,7 @@
         "N:D377Y"
     ],
     "rules": {
-        "min_alt": 8,
-        "max_ref": 17
+        "min_alt": 9,
+        "max_ref": 3
     }
 }
diff --git a/constellations/definitions/cP.1.json b/constellations/definitions/cP.1.json
@@ -38,7 +38,7 @@
         "N:P80R"
     ],
     "rules": {
-        "min_alt": 5,
-        "max_ref": 16
+        "min_alt": 8,
+        "max_ref": 3
     }
 }
diff --git a/constellations/definitions/cP.2.json b/constellations/definitions/cP.2.json
@@ -28,7 +28,7 @@
         "N:M234I"
     ],
     "rules": {
-        "min_alt": 6,
-        "max_ref": 6
+        "min_alt": 5,
+        "max_ref": 1
     }
 }
diff --git a/constellations/definitions/cP.3.json b/constellations/definitions/cP.3.json
@@ -39,7 +39,7 @@
         "nuc:T24187A"
     ],
     "rules": {
-        "min_alt": 7,
-        "max_ref": 17
+        "min_alt": 9,
+        "max_ref": 3
     }
 }