From 1ad712f09686d8fb62af289d21b84e17fd948649 Mon Sep 17 00:00:00 2001
From: ivan-aksamentov <ivan.aksamentov@gmail.com>
Date: Tue, 13 Feb 2024 09:13:25 +0100
Subject: [PATCH] chore: release cli and web 3.2.0

---
 CHANGELOG.md                        | 22 ++++++++++++++++++++++
 Cargo.lock                          |  6 +++---
 packages/nextclade-cli/Cargo.toml   |  2 +-
 packages/nextclade-web/Cargo.toml   |  2 +-
 packages/nextclade-web/package.json |  2 +-
 packages/nextclade/Cargo.toml       |  2 +-
 6 files changed, 29 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 009ee5c7a..36b5170e4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,25 @@
+## Nextclade 3.2.0
+
+### General
+
+#### Minimizer search algorithm configuration has been improved
+
+Minimizer search algorithm used in dataset auto-suggestion in Nextclade Web as well as in `sort` command of Nextclade CLI.
+
+The default value for minimum match score (`--min-score`) has been reduced from 0.3 to 0.1. The default value for minimum number of hits (`--min-hits`) required for a detection has been reduced from 10 to 5. This should allow to better handle more diverse viruses.
+
+If there is a sufficiently large gap between dataset scores, the algorithm will now only consider the group of datasets before the gap. The gap size can be configured using `--max-score-gap` argument in Nextclade CLI. The default value is `0.2`.
+
+Additionally, in Nextclade CLI `sort` command the algorithm now chooses only the best matching dataset. In order to select all matching datasets, the `--all-matches` flag has been added.
+
+
+### Nextclade CLI
+
+#### Sequence index in the output TSV file of the `sort` command
+
+The TSV output of the `sort` command (requested with `--output-results-tsv`) now contains additional column: `index`. The cells under this column contain index of the corresponding input sequence in the FASTA file. These indices can be used in the downstream processing to reliably map input sequences to the output results. Sequence names alone can be unreliable because they are arbitrary strings which are not guaranteed to be unique.
+
+
 ## Nextclade 3.1.0
 
 ### CLI
diff --git a/Cargo.lock b/Cargo.lock
index 146eb19a4..6e1f2b5bd 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1711,7 +1711,7 @@ dependencies = [
 
 [[package]]
 name = "nextclade"
-version = "3.1.0"
+version = "3.2.0"
 dependencies = [
  "assert2",
  "atty",
@@ -1775,7 +1775,7 @@ dependencies = [
 
 [[package]]
 name = "nextclade-cli"
-version = "3.1.0"
+version = "3.2.0"
 dependencies = [
  "assert2",
  "clap",
@@ -1818,7 +1818,7 @@ dependencies = [
 
 [[package]]
 name = "nextclade-web"
-version = "3.1.0"
+version = "3.2.0"
 dependencies = [
  "assert2",
  "chrono",
diff --git a/packages/nextclade-cli/Cargo.toml b/packages/nextclade-cli/Cargo.toml
index dd1354fbe..1aa8e5eb5 100644
--- a/packages/nextclade-cli/Cargo.toml
+++ b/packages/nextclade-cli/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "nextclade-cli"
-version = "3.1.0"
+version = "3.2.0"
 description = "Alignment, mutation calling, phylogenetic placement, clade assignment and quality control checks for viral genetic sequences. CLI module."
 repository = "https://github.com/nextstrain/nextclade"
 documentation = "https://docs.nextstrain.org/projects/nextclade/en/stable/"
diff --git a/packages/nextclade-web/Cargo.toml b/packages/nextclade-web/Cargo.toml
index f51458e4f..57c2ff608 100644
--- a/packages/nextclade-web/Cargo.toml
+++ b/packages/nextclade-web/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "nextclade-web"
-version = "3.1.0"
+version = "3.2.0"
 description = "Alignment, mutation calling, phylogenetic placement, clade assignment and quality control checks for viral genetic sequences. WebAssembly module."
 edition = "2021"
 license = "MIT"
diff --git a/packages/nextclade-web/package.json b/packages/nextclade-web/package.json
index 45ae1f66f..87e70e276 100644
--- a/packages/nextclade-web/package.json
+++ b/packages/nextclade-web/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@nextstrain/nextclade-web",
-  "version": "3.1.0",
+  "version": "3.2.0",
   "description": "Clade assignment, mutation calling, and sequence quality checks",
   "homepage": "https://clades.nextstrain.org",
   "repository": {
diff --git a/packages/nextclade/Cargo.toml b/packages/nextclade/Cargo.toml
index 5977f5e66..68194acf7 100644
--- a/packages/nextclade/Cargo.toml
+++ b/packages/nextclade/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "nextclade"
-version = "3.1.0"
+version = "3.2.0"
 description = "Alignment, mutation calling, phylogenetic placement, clade assignment and quality control checks for viral genetic sequences. Library module."
 repository = "https://github.com/nextstrain/nextclade"
 documentation = "https://docs.nextstrain.org/projects/nextclade/en/stable/"