From 05269d0fb084de2b888378cfa53b98efbf58001d Mon Sep 17 00:00:00 2001
From: Kim Andrews <17375001+kimandrews@users.noreply.github.com>
Date: Wed, 1 May 2024 13:45:37 -0700
Subject: [PATCH] Add QC parameters to `pathogen.json`

---
 nextclade_dataset/pathogen.json | 26 ++++++++++++++++++++++----
 1 file changed, 22 insertions(+), 4 deletions(-)

diff --git a/nextclade_dataset/pathogen.json b/nextclade_dataset/pathogen.json
index 2315ebf..b52ddcf 100644
--- a/nextclade_dataset/pathogen.json
+++ b/nextclade_dataset/pathogen.json
@@ -8,8 +8,26 @@
 	"attributes": {
 	  "name": "Measles"
 	},
-	"schemaVersion": "3.0.0",
-	"version": {
-	  "tag": "unreleased"
-	}
+	"schemaVersion": "1.0.0",
+	"alignmentParams": {
+		"minSeedCover": 0.01,
+		"minLength": 400
+	  },
+    "qc": {
+		"missingData": {
+		  "enabled": true,
+		  "missingDataThreshold": 20,
+		  "scoreBias": 4
+		},
+		"mixedSites": {
+		  "enabled": true,
+		  "mixedSitesThreshold": 4
+		},
+		"frameShifts": {
+		  "enabled": true
+		},
+		"stopCodons": {
+		  "enabled": true
+		}
+	  }
   }