From 0bab6f02121af876e4ae841b8a837129cf0fc4e5 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Tue, 21 Mar 2023 09:29:46 +0100 Subject: [PATCH] chore: release cli and web 2.13.0 --- CHANGELOG.md | 10 +++++----- Cargo.lock | 6 +++--- packages_rs/nextclade-cli/Cargo.toml | 2 +- packages_rs/nextclade-web/Cargo.toml | 2 +- packages_rs/nextclade-web/package.json | 2 +- packages_rs/nextclade/Cargo.toml | 2 +- 6 files changed, 12 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2941bb86b..4edbe6686 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -## Upcoming +## Nextclade Web 2.13.0, Nextclade CLI 2.13.0 (2023-03-21) ### Attach sequences to a priori most likely node if reference tree contains "placement_prior" @@ -6,17 +6,17 @@ Until now, when there were multiple positions with equal numbers of mismatches b In this version, we introduce a new [feature](https://github.com/nextstrain/nextclade/pull/1119) that allows to attach sequences to a priori most likely nodes - taking into account which positions on the reference tree are most commonly found in circulation. The information on the prior probability that a particular reference tree node is the best match for a random query sequence is contained in the `placement_prior` reference tree node attribute. This attribute is currently only present in the most recent SARS-CoV-2 reference trees. The calculation can be found in this `nextclade_data_workflows` [pull request](https://github.com/neherlab/nextclade_data_workflows/pull/38). -To given an example: a partial sequence may have as many mismatches when compared to BA.5 as it has to the recombinant XP. Based on sequences in public databases, we know that BA.5 is much more common than XP. Hence, the query sequence is attached to BA.5. Previously, the query sequence would have been attached to XP, because XP has fewer parent nodes in the reference tree. +To give an example: a partial sequence may have as many mismatches when compared to BA.5 as it has to the recombinant XP. Based on sequences in public databases, we know that BA.5 is much more common than XP. Hence, the query sequence is attached to BA.5. Previously, the query sequence would have been attached to XP, because XP has fewer parent nodes in the reference tree. The impact of the feature is biggest for partial and incomplete sequences. ### Add custom phenotype values to the newly placed tree nodes -The phenotype values (such as `ace2_binding` and `"immune_escape"`) are present in all output files, but are missing from the tree JSON, due to an omission. This is no fixed and these values are set as node attributes of the tree. This allows to see the values and colorings for phenotype values on the tree page. +When available in the dataset, the phenotype values (such as `ace2_binding` and `immune_escape`) are written into all output files except Auspice tree JSON. This omission is now fixed, and these values are set as tree node attributes. This allows to see the values and colorings for phenotype values on the tree page, and when loading the output tree JSON file into Auspice. ### Fix length of 3' unsequenced aminoacid ranges in Nextclade Web -Nextclade Web was showing right boundary of the unsequenced AA range on the 3' end of peptide sequences incorrectly (the range was longer than expected). The calculations were using length of a gene in nuc;eotides, where there should be length in codons. This is now fixed. +Nextclade Web was showing right boundary of the unsequenced AA range on the 3' end of peptide sequences incorrectly - the range was longer than expected. The calculations were using length of a gene in nucleotides, where there should be length in codons. This is now fixed. ### Fix incorrect indices in mutation badges @@ -28,7 +28,7 @@ The `input-pcr-primers` and `input-virus-properties` URL params were swapped in ### Ensure translation warnings in CLI -Due to an omission, Nextclade CLI and Nextalign CLI since v2 did not print sequence translation-releated warnings to the console. This is now fixed. +Due to an omission, Nextclade CLI and Nextalign CLI since v2 did not print sequence translation-related warnings to the console. This is now fixed. ### Fix Google Search Console warnings diff --git a/Cargo.lock b/Cargo.lock index 3ec7f0439..233092760 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1449,7 +1449,7 @@ dependencies = [ [[package]] name = "nextclade" -version = "2.12.0" +version = "2.13.0" dependencies = [ "assert2", "atty", @@ -1501,7 +1501,7 @@ dependencies = [ [[package]] name = "nextclade-cli" -version = "2.12.0" +version = "2.13.0" dependencies = [ "assert2", "clap 3.1.18", @@ -1539,7 +1539,7 @@ dependencies = [ [[package]] name = "nextclade-web" -version = "2.12.0" +version = "2.13.0" dependencies = [ "assert2", "console_error_panic_hook", diff --git a/packages_rs/nextclade-cli/Cargo.toml b/packages_rs/nextclade-cli/Cargo.toml index c5a149274..12bf47e05 100644 --- a/packages_rs/nextclade-cli/Cargo.toml +++ b/packages_rs/nextclade-cli/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "nextclade-cli" -version = "2.12.0" +version = "2.13.0" 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_rs/nextclade-web/Cargo.toml b/packages_rs/nextclade-web/Cargo.toml index 71c77db6d..becd7dd1a 100644 --- a/packages_rs/nextclade-web/Cargo.toml +++ b/packages_rs/nextclade-web/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "nextclade-web" -version = "2.12.0" +version = "2.13.0" 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_rs/nextclade-web/package.json b/packages_rs/nextclade-web/package.json index 7715a9b0f..3970f7d60 100644 --- a/packages_rs/nextclade-web/package.json +++ b/packages_rs/nextclade-web/package.json @@ -1,6 +1,6 @@ { "name": "@nextstrain/nextclade-web", - "version": "2.12.0", + "version": "2.13.0", "description": "Clade assignment, mutation calling, and sequence quality checks", "homepage": "https://clades.nextstrain.org", "repository": { diff --git a/packages_rs/nextclade/Cargo.toml b/packages_rs/nextclade/Cargo.toml index 9added3e0..6666339d0 100644 --- a/packages_rs/nextclade/Cargo.toml +++ b/packages_rs/nextclade/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "nextclade" -version = "2.12.0" +version = "2.13.0" 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/"