From 7501de4f054052a657c7d4410cc2deecc7975112 Mon Sep 17 00:00:00 2001 From: rambaut Date: Thu, 3 Jun 2021 18:16:06 +0100 Subject: [PATCH] adjusting definition rules --- constellations/definitions/cA.23.1+E484K.json | 2 +- constellations/definitions/cA.23.1.json | 2 +- constellations/definitions/cAV1.json | 4 +-- constellations/definitions/cB.1.1.318.json | 4 +-- .../definitions/cB.1.1.7+E484K.json | 4 +-- constellations/definitions/cB.1.1.7.json | 4 +-- constellations/definitions/cB.1.324.1.json | 4 +-- constellations/definitions/cB.1.351.json | 4 +-- constellations/definitions/cB.1.427_429.json | 16 ++++++++++-- constellations/definitions/cB.1.525.json | 4 +-- constellations/definitions/cB.1.526.json | 26 ++++++++++++++++--- constellations/definitions/cB.1.617.1.json | 2 +- .../definitions/cB.1.617.2+K417N.json | 2 +- constellations/definitions/cB.1.617.2.json | 2 +- constellations/definitions/cB.1.617.3.json | 4 +-- constellations/definitions/cP.1.json | 4 +-- constellations/definitions/cP.2.json | 4 +-- constellations/definitions/cP.3.json | 4 +-- 18 files changed, 64 insertions(+), 32 deletions(-) diff --git a/constellations/definitions/cA.23.1+E484K.json b/constellations/definitions/cA.23.1+E484K.json index 1822a07..eda3483 100644 --- 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" } } \ No newline at end of file diff --git a/constellations/definitions/cA.23.1.json b/constellations/definitions/cA.23.1.json index ad891b5..d6756d5 100644 --- 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 } } \ No newline at end of file diff --git a/constellations/definitions/cAV1.json b/constellations/definitions/cAV1.json index d73fcc2..020a5b1 100644 --- 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 index 440faff..3d9b901 100644 --- 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 } } \ No newline at end of file diff --git a/constellations/definitions/cB.1.1.7+E484K.json b/constellations/definitions/cB.1.1.7+E484K.json index 3d04d30..81d21a2 100644 --- 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 index f377830..6d8899a 100644 --- 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 index 00f0119..3afd455 100644 --- 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 } } \ No newline at end of file diff --git a/constellations/definitions/cB.1.351.json b/constellations/definitions/cB.1.351.json index 543a43f..7e7888b 100644 --- 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 index 134959c..7e7442b 100644 --- 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 } -} \ No newline at end of file +} + diff --git a/constellations/definitions/cB.1.525.json b/constellations/definitions/cB.1.525.json index 782b70f..5d41493 100644 --- 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 } } \ No newline at end of file diff --git a/constellations/definitions/cB.1.526.json b/constellations/definitions/cB.1.526.json index ab22c5d..8169aeb 100644 --- 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 } -} \ No newline at end of file +} + diff --git a/constellations/definitions/cB.1.617.1.json b/constellations/definitions/cB.1.617.1.json index 83a08c4..c931c29 100644 --- 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 index 74f1504..d83a069 100644 --- 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 index f826666..6069496 100644 --- 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 index a860c7b..68d5b5b 100644 --- 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 } } \ No newline at end of file diff --git a/constellations/definitions/cP.1.json b/constellations/definitions/cP.1.json index 125df3b..b02231f 100644 --- 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 index a582b99..134fddc 100644 --- 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 index 0e772c1..3c49e34 100644 --- 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 } } \ No newline at end of file