Bug fix release for flu_yam_ha

CHANGELOG.md

@@ -1,4 +1,14 @@
-## 2022-07-26
+## 2022-07-27
+
+### Influenza Yamagata HA
+
+#### Bug fix release (tag `2022-07-27T12:00:00Z`)
+
+Fix: The old tree used an incorrect genemap which caused Nextclade to crash. Now it works again.
+
+Beware that Nextclade v2.0.0 until v2.3.0 have had a bug that means this dataset will crash.
+
+You will have to upgrade to Nextclade v2.3.1 or use Nextclade v1 to use this dataset.
 
 ### SARS-CoV-2 and SARS-CoV-2-no-recomb
 

data/datasets/flu_yam_ha/references/JN993010/versions/2022-07-27T12:00:00Z/files/genemap.gff

@@ -0,0 +1,5 @@
+##gff-version 3
+##sequence-region JN993010.1 1 1755
+JN993010.1	feature	gene	1	45	.	+	.	gene_name=SigPep
+JN993010.1	feature	gene	46	1083	.	+	.	gene_name=HA1
+JN993010.1	feature	gene	1084	1755	.	+	.	gene_name=HA2

data/datasets/flu_yam_ha/references/JN993010/versions/2022-07-27T12:00:00Z/files/primers.csv

@@ -0,0 +1 @@
+Country (Institute),Target,Oligonucleotide,Sequence

data/datasets/flu_yam_ha/references/JN993010/versions/2022-07-27T12:00:00Z/files/qc.json

@@ -0,0 +1,30 @@
+{
+  "schemaVersion": "1.2.0",
+  "privateMutations": {
+    "enabled": true,
+    "typical": 5,
+    "cutoff": 15
+  },
+  "missingData": {
+    "enabled": false,
+    "missingDataThreshold": 100,
+    "scoreBias": 10
+  },
+  "snpClusters": {
+    "enabled": false,
+    "windowSize": 100,
+    "clusterCutOff": 5,
+    "scoreWeight": 50
+  },
+  "mixedSites": {
+    "enabled": true,
+    "mixedSitesThreshold": 4
+  },
+  "frameShifts": {
+    "enabled": true
+  },
+  "stopCodons": {
+    "enabled": true,
+    "ignoredStopCodons": []
+  }
+}

data/datasets/flu_yam_ha/references/JN993010/versions/2022-07-27T12:00:00Z/files/reference.fasta

@@ -0,0 +1,2 @@
+>JN993010.1 Influenza B virus (B/Wisconsin/01/2010) segment 4 hemagglutinin (HA) gene, complete cds
+ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCGGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGGCCAATGTGTGTGGGGACCACACCTTCTGCTAAAGCTTCAATACTCCACGAGGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAAGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAATCGGATTTTTTGCAACAATGGCTTGGGCTGTCCCAAAGGACAACTACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAGCCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGACTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTAAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTGAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCAGACCTTAAGAGTACACAAGAAGCTATAAATAAGATAACAAAAAATCTCAATTCTTTGAGTGAGCTAGAAGTAAAGAACCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAACGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTAATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA

data/datasets/flu_yam_ha/references/JN993010/versions/2022-07-27T12:00:00Z/files/tag.json

@@ -0,0 +1,25 @@
+{
+  "tag": "2022-06-27T12:00:00Z",
+  "comment": "fix: tree now uses correct genemap",
+  "compatibility": {
+    "nextcladeCli": {
+      "min": "1.10.0",
+      "max": null
+    },
+    "nextcladeWeb": {
+      "min": "1.13.0",
+      "max": null
+    }
+  },
+  "enabled": true,
+  "files": {
+    "geneMap": "genemap.gff",
+    "primers": "primers.csv",
+    "qc": "qc.json",
+    "reference": "reference.fasta",
+    "sequences": "sequences.fasta",
+    "tree": "tree.json",
+    "virusPropertiesJson": "virus_properties.json"
+  },
+  "metadata": {}
+}