adjusting definition rules

rambaut · rambaut · commit 7501de4f0540 · 2021-06-03T18:16:06.000+01:00
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
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -34,7 +34,7 @@`
`34`	`34`	`],`
`35`	`35`	`"rules": {`
`36`	`36`	`"min_alt": 5,`
`37`		`- "max_ref": 13,`
	`37`	`+ "max_ref": 3,`
`38`	`38`	`"S:E484K": "alt"`
`39`	`39`	`}`
`40`	`40`	`}`
Original file line number	Diff line number	Diff line change
`@@ -30,6 +30,6 @@`
`30`	`30`	`],`
`31`	`31`	`"rules": {`
`32`	`32`	`"min_alt": 5,`
`33`		`- "max_ref": 13`
	`33`	`+ "max_ref": 3`
`34`	`34`	`}`
`35`	`35`	`}`
Original file line number	Diff line number	Diff line change
`@@ -32,7 +32,7 @@`
`32`	`32`	`"N:G204R"`
`33`	`33`	`],`
`34`	`34`	`"rules": {`
`35`		`- "min_alt": 6,`
`36`		`- "max_ref": 0`
	`35`	`+ "min_alt": 7,`
	`36`	`+ "max_ref": 3`
`37`	`37`	`}`
`38`	`38`	`}`
Original file line number	Diff line number	Diff line change
`@@ -39,7 +39,7 @@`
`39`	`39`	`"del:28895:3"`
`40`	`40`	`],`
`41`	`41`	`"rules": {`
`42`		`- "min_alt": 5,`
`43`		`- "max_ref": 19`
	`42`	`+ "min_alt": 11,`
	`43`	`+ "max_ref": 3`
`44`	`44`	`}`
`45`	`45`	`}`
Original file line number	Diff line number	Diff line change
`@@ -42,8 +42,8 @@`
`42`	`42`	`"N:S235F"`
`43`	`43`	`],`
`44`	`44`	`"rules": {`
`45`		`- "min_alt": 5,`
`46`		`- "max_ref": 4,`
	`45`	`+ "min_alt": 15,`
	`46`	`+ "max_ref": 3,`
`47`	`47`	`"S:E484K": "alt"`
`48`	`48`	`}`
`49`	`49`	`}`
Original file line number	Diff line number	Diff line change
`@@ -43,7 +43,7 @@`
`43`	`43`	`"N:S235F"`
`44`	`44`	`],`
`45`	`45`	`"rules": {`
`46`		`- "min_alt": 4,`
`47`		`- "max_ref": 6`
	`46`	`+ "min_alt": 15,`
	`47`	`+ "max_ref": 3`
`48`	`48`	`}`
`49`	`49`	`}`
Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,7 @@`
`29`	`29`	`"nuc:A28272T"`
`30`	`30`	`],`
`31`	`31`	`"rules": {`
`32`		`- "min_alt": 8,`
`33`		`- "max_ref": 9`
	`32`	`+ "min_alt": 5,`
	`33`	`+ "max_ref": 3`
`34`	`34`	`}`
`35`	`35`	`}`
Original file line number	Diff line number	Diff line change
`@@ -40,7 +40,7 @@`
`40`	`40`	`"nuc:G29543T"`
`41`	`41`	`],`
`42`	`42`	`"rules": {`
`43`		`- "min_alt": 5,`
`44`		`- "max_ref": 16`
	`43`	`+ "min_alt": 8,`
	`44`	`+ "max_ref": 3`
`45`	`45`	`}`
`46`	`46`	`}`