From 9e19e2cdebf740cadace53949e4e2ace61b27ebd Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Thu, 17 Oct 2024 10:30:28 -0700
Subject: [PATCH] Update nextclade files based on PR feedback

Context: https://github.com/nextstrain/nextclade_data/pull/220
---
 nextclade/defaults/nextclade-dataset/CHANGELOG.md  | 2 +-
 nextclade/defaults/nextclade-dataset/README.md     | 4 ++--
 nextclade/defaults/nextclade-dataset/pathogen.json | 7 +++----
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/nextclade/defaults/nextclade-dataset/CHANGELOG.md b/nextclade/defaults/nextclade-dataset/CHANGELOG.md
index 3b67234..eb62595 100644
--- a/nextclade/defaults/nextclade-dataset/CHANGELOG.md
+++ b/nextclade/defaults/nextclade-dataset/CHANGELOG.md
@@ -1,3 +1,3 @@
 ## Unreleased
 
-Initial release of yellow fever virus dataset.
+Initial release of yellow fever virus (prM-E region only) dataset.
diff --git a/nextclade/defaults/nextclade-dataset/README.md b/nextclade/defaults/nextclade-dataset/README.md
index 10bb176..1a22958 100644
--- a/nextclade/defaults/nextclade-dataset/README.md
+++ b/nextclade/defaults/nextclade-dataset/README.md
@@ -1,4 +1,4 @@
-# Yellow fever virus dataset
+# Yellow fever virus (prM-E region only) dataset
 
 | Key               | Value                                                            |
 | ----------------- | -----------------------------------------------------------------|
@@ -36,7 +36,7 @@ following genotypes as described in the aforementioned two papers:
 
 (N.b., the reference sequence used in this data set is actually 672nt
 long, from bases 641-1312 of the genome reference. The 2 extra bases
-make the reference an complete open reading frame.)
+make the reference a complete open reading frame.)
 
 This dataset can be used to assign genotypes to any sequence that
 includes at least 500 bp of the prM-E region, including whole genome
diff --git a/nextclade/defaults/nextclade-dataset/pathogen.json b/nextclade/defaults/nextclade-dataset/pathogen.json
index 92213e6..b1d1212 100644
--- a/nextclade/defaults/nextclade-dataset/pathogen.json
+++ b/nextclade/defaults/nextclade-dataset/pathogen.json
@@ -15,8 +15,7 @@
   },
   "schemaVersion": "3.0.0",
   "alignmentParams": {
-      "minSeedCover": 0.01,
-      "minLength": 500
+      "minSeedCover": 0.01
   },
   "qc": {
     "missingData": {
@@ -36,8 +35,8 @@
     },
     "privateMutations": {
       "enabled": true,
-      "cutoff": 8,
-      "typical": 2,
+      "cutoff": 12,
+      "typical": 4,
       "weightLabeledSubstitutions": 1,
       "weightReversionSubstitutions": 1,
       "weightUnlabeledSubstitutions": 1