Merge pull request #62 from cov-lineages/dev

Dev
cov-lineages · Apr 22, 2022 · 6a58cd0 · 6a58cd0
2 parents d243a24 + 5ae2e9b
commit 6a58cd0
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Showing 7 changed files with 9 additions and 13 deletions.
diff --git a/constellations/__init__.py b/constellations/__init__.py
@@ -1,3 +1,3 @@
 _program = "constellations"
-__version__ = "v0.1.7"
+__version__ = "v0.1.8"
 
diff --git a/constellations/definitions/cBA.2.json b/constellations/definitions/cBA.2.json
@@ -29,7 +29,6 @@
         "orf1ab:SGF3675-",
         "nuc:C10198T",
         "nuc:G10447A",
-        "nuc:C15714T",
         "nuc:C12880T",
         "nuc:C15714T",
         "orf1ab:R5716C",
@@ -54,7 +53,7 @@
     "note": "Unique mutations for sublineage",
     "rules": {
       "default": {
-        "min_alt": 28,
+        "min_alt": 27,
         "max_ref": 3,
         "spike:Q493":"alt",
         "n:P151":"ref",

diff --git a/constellations/definitions/cBA.3.json b/constellations/definitions/cBA.3.json
@@ -27,7 +27,6 @@
         "nuc:C11235T",
         "nuc:C12880T",
         "nuc:C15714T",
-        "orf1ab:I5967V",
         "spike:A67V",
         "spike:Q493R",
         "del:21765:6",
@@ -44,7 +43,7 @@
     "note": "Unique mutations for sublineage",
     "rules": {
       "default": {
-        "min_alt": 14,
+        "min_alt": 13,
         "max_ref": 2
       },
       "Probable": {

diff --git a/constellations/definitions/cBA.4.json b/constellations/definitions/cBA.4.json
@@ -34,7 +34,6 @@
       "nuc:A20055G",
       "spike:T19I",
       "s:HV69-",
-      "nuc:T22200G",
       "spike:V213G",
       "spike:S371F",
       "spike:T376A",
@@ -54,7 +53,7 @@
     "note": "Unique mutations for sublineage",
     "rules": {
       "default": {
-        "min_alt": 30,
+        "min_alt": 29,
         "max_ref": 5,
         "m:D3N":"ref",
         "s:Q493":"ref",

diff --git a/constellations/definitions/cBA.5.json b/constellations/definitions/cBA.5.json
@@ -34,7 +34,6 @@
       "nuc:A20055G",
       "spike:T19I",
       "s:HV69-",
-      "nuc:T22200G",
       "spike:V213G",
       "spike:S371F",
       "spike:T376A",
@@ -51,7 +50,7 @@
     "note": "Unique mutations for sublineage",
     "rules": {
       "default": {
-        "min_alt": 28,
+        "min_alt": 27,
         "max_ref": 5,
         "s:Q493":"ref",
         "nuc:C26858":"ref",

diff --git a/constellations/definitions/cXE-parent2.json b/constellations/definitions/cXE-parent2.json
@@ -19,7 +19,6 @@
     "sites": [
         "nuc:C15714T",
         "nuc:C12880T",
-        "nuc:C15714T",
         "orf1ab:R5716C",
         "orf1ab:T6564I",
         "nuc:A20055G",
@@ -39,7 +38,7 @@
     ],
     "rules": {
       "default": {
-        "min_alt": 9,
+        "min_alt": 8,
         "max_ref": 3
       }
     }

diff --git a/constellations/definitions/cXE.json b/constellations/definitions/cXE.json
@@ -22,9 +22,10 @@
     "sites": [
     "nuc:C3241T",
     "nuc:T5386G",
-	"nuc:C14599T",
+    "nuc:C14599T",
     "nuc:C12880T",
-    "nuc:A29510C"
+    "nuc:A29510C",
+    "nuc:C14599T"
     ],
     "rules": {
         "min_alt": 2,