From 1ee5ac5a10a73147df50c1dc4942ba2db9b1f6c6 Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Fri, 26 Jan 2024 11:52:00 -0800
Subject: [PATCH] fixup: alignment params

---
 nextclade_data/denv1/pathogen.json | 4 +++-
 nextclade_data/denv2/pathogen.json | 3 ++-
 nextclade_data/denv3/pathogen.json | 3 ++-
 nextclade_data/denv4/pathogen.json | 3 ++-
 4 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/nextclade_data/denv1/pathogen.json b/nextclade_data/denv1/pathogen.json
index 7aae8ea0..da53831c 100644
--- a/nextclade_data/denv1/pathogen.json
+++ b/nextclade_data/denv1/pathogen.json
@@ -1,6 +1,8 @@
 {
   "alignmentParams": {
-    "minSeedCover": 0.01
+    "minSeedCover": 0.1,
+    "minLength": 1000,
+    "mismatchesAllowed": 2000
   },
   "attributes": {
     "name": "Dengue virus DENV1 dataset",
diff --git a/nextclade_data/denv2/pathogen.json b/nextclade_data/denv2/pathogen.json
index 5a6da634..c3ce2c45 100644
--- a/nextclade_data/denv2/pathogen.json
+++ b/nextclade_data/denv2/pathogen.json
@@ -1,6 +1,7 @@
 {
   "alignmentParams": {
-    "minSeedCover": 0.01
+    "minSeedCover": 0.1,
+    "minLength": 1000
   },
   "attributes": {
     "name": "Dengue virus DENV2 dataset",
diff --git a/nextclade_data/denv3/pathogen.json b/nextclade_data/denv3/pathogen.json
index 2cac79b1..b4396cdb 100644
--- a/nextclade_data/denv3/pathogen.json
+++ b/nextclade_data/denv3/pathogen.json
@@ -1,6 +1,7 @@
 {
   "alignmentParams": {
-    "minSeedCover": 0.01
+    "minSeedCover": 0.1,
+    "minLength": 1000
   },
   "attributes": {
     "name": "Dengue virus DENV3 dataset",
diff --git a/nextclade_data/denv4/pathogen.json b/nextclade_data/denv4/pathogen.json
index ccd38ccd..6d88d4f4 100644
--- a/nextclade_data/denv4/pathogen.json
+++ b/nextclade_data/denv4/pathogen.json
@@ -1,6 +1,7 @@
 {
   "alignmentParams": {
-    "minSeedCover": 0.01
+    "minSeedCover": 0.1,
+    "minLength": 1000
   },
   "attributes": {
     "name": "Dengue virus DENV4 dataset",