From e97dc0e3168371b934988ee9d9a67891efb58a5f Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Mon, 24 Jan 2022 12:54:02 +0100 Subject: [PATCH 01/13] chore: CHANGELOG 1.13.0 --- CHANGELOG.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fc3e80611..c961ec576 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,19 @@ +## Nextclade Web 1.13.0, Nextclade CLI 1.10.0, Nextalign CLI 1.10.0 (2022-01-24) + +### [Feature] Detailed split of private mutations + +Private mutations (differences between a query sequence and nearest neighbour in reference tree) are now split into three categories: + +1. Reversion to reference genotype +2. (SARS-CoV-2 only for now) Mutation to a genotype common in at least 1 clade get labeled with that clade +3. Mutations that are neither reversions nor labeled (called "unlabeled" + +Which category a mutation belongs to is visible by hovering over the "divergence" column (in web) and in various "privateNucMutations" fields in [csv/tsv/json outputs](https://docs.nextstrain.org/projects/nextclade/en/latest/user/output-files.html#tabular-csv-tsv-results). + +### [Change] Rare mutations QC rule now uses reversion and labeled mutation counts + +Reversions and labeled mutations (see feature above) are particularly common in contaminated samples, coinfections and recombination. To draw the user's attention to such sequences, both types of private mutation now get higher weights private mutation QC rule. + ## Nextclade Web 1.12.0, Nextclade CLI 1.9.0, Nextalign CLI 1.9.0 (2022-01-11) ### [Feature] Handle "-" strand gene translation From 0ef2091fc259a3c8b88d63e25b23deb974345e8d Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Mon, 24 Jan 2022 13:15:28 +0100 Subject: [PATCH 02/13] chore: add aa insertion to CHANGELOG --- CHANGELOG.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c961ec576..8a6ad7db7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ ## Nextclade Web 1.13.0, Nextclade CLI 1.10.0, Nextalign CLI 1.10.0 (2022-01-24) -### [Feature] Detailed split of private mutations +### [Feature] Detailed split of private mutations (Nextclade) [#698](https://github.com/nextstrain/nextclade/pull/689) Private mutations (differences between a query sequence and nearest neighbour in reference tree) are now split into three categories: @@ -10,7 +10,11 @@ Private mutations (differences between a query sequence and nearest neighbour in Which category a mutation belongs to is visible by hovering over the "divergence" column (in web) and in various "privateNucMutations" fields in [csv/tsv/json outputs](https://docs.nextstrain.org/projects/nextclade/en/latest/user/output-files.html#tabular-csv-tsv-results). -### [Change] Rare mutations QC rule now uses reversion and labeled mutation counts +### [Feature] Insertions now also available as amino acids [#692](https://github.com/nextstrain/nextclade/pull/692) + +Nucleotide insertions are now additionally translated into amino acids. You can find them by hovering over the "insertions" column in the web app and as "aaInsertions" and "totalAminoacidInsertions" fields in Nextalign and Nextclade output. + +### [Change] Rare mutations QC rule now uses reversion and labeled mutation counts (Nextclade) Reversions and labeled mutations (see feature above) are particularly common in contaminated samples, coinfections and recombination. To draw the user's attention to such sequences, both types of private mutation now get higher weights private mutation QC rule. From 6b0cc9c20cf2162642dfbc47b2c710eea54398e7 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Mon, 24 Jan 2022 13:16:52 +0100 Subject: [PATCH 03/13] chore: fix PR number in changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8a6ad7db7..c617f5c08 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ ## Nextclade Web 1.13.0, Nextclade CLI 1.10.0, Nextalign CLI 1.10.0 (2022-01-24) -### [Feature] Detailed split of private mutations (Nextclade) [#698](https://github.com/nextstrain/nextclade/pull/689) +### [Feature] Detailed split of private mutations (Nextclade) [#689](https://github.com/nextstrain/nextclade/pull/689) Private mutations (differences between a query sequence and nearest neighbour in reference tree) are now split into three categories: From bcac461d3a4a9fb1860536b31611165883f8e9ea Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Mon, 24 Jan 2022 13:18:40 +0100 Subject: [PATCH 04/13] chore: remove superfluous newlines in CHANGELOG --- CHANGELOG.md | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c617f5c08..85c8cbfa3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -44,14 +44,12 @@ The alignment algorithm in Nextclade CLI and Nextalign CLI could sometimes produ In rare cases Nextclade and Nextalign algorithms could sometimes read past the end of arrays, which previously went undetected. This is now fixed. - ## Nextclade Web 1.11.1, Nextclade CLI 1.8.1 (2022-01-07) ### [Hotfix] Nextclade CLI crashes on macOS when reading JSON tree (#680) Fixes crash `Error: [json.exception.invalid_iterator.214] cannot get value |` when reading JSON tree on macOS - ## Nextclade Web 1.11.0, Nextclade CLI 1.8.0 (2022-01-04) ### [Feature] Better dataset selector @@ -64,7 +62,7 @@ Nextclade CLI and Nextclade Web now can assign multiple clade-like attributes to If input reference tree JSON contains an array of attribute keys attached to the -``` +```js meta.extensions.nextclade.clade_node_attrs_keys = ["my_clades", "other_clades"] ``` @@ -85,10 +83,8 @@ The new optimized FASTA parser makes Nextclade CLI up to 60% faster and Nextalig This is an internal fix of a problem that might have lead to a crash in rare cases, when coordinate map array was accessed beyond it's size. - ## Nextclade Web 1.9.0, Nextclade CLI 1.6.0 (2021-12-07) - ### [BREAKING CHANGE] [Fix] Remove unused CLI flags for aminoacid seed alignment Seed matching step was removed in Nextalign and Nextclade CLI 1.5.0, however the command-line parameters previously providing configuration options for this step were not. In this version, the now unused family of `--aa-*` CLI flags is removed. Migration path: remove these flags from Nextclade CLI invocation. From e4ddff8c54f9c3753166165ca0e5cef9ee4755ab Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Mon, 24 Jan 2022 13:47:03 +0100 Subject: [PATCH 05/13] chore: fix typo, missing ) in CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 85c8cbfa3..1d90bb31c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,7 @@ Private mutations (differences between a query sequence and nearest neighbour in 1. Reversion to reference genotype 2. (SARS-CoV-2 only for now) Mutation to a genotype common in at least 1 clade get labeled with that clade -3. Mutations that are neither reversions nor labeled (called "unlabeled" +3. Mutations that are neither reversions nor labeled (called "unlabeled") Which category a mutation belongs to is visible by hovering over the "divergence" column (in web) and in various "privateNucMutations" fields in [csv/tsv/json outputs](https://docs.nextstrain.org/projects/nextclade/en/latest/user/output-files.html#tabular-csv-tsv-results). From 6790b4adf610d2549ed1c415684cc681b63666c7 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Mon, 24 Jan 2022 14:18:21 +0100 Subject: [PATCH 06/13] chore: fix typo (missing words) in CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1d90bb31c..5d4c4cd29 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ Nucleotide insertions are now additionally translated into amino acids. You can ### [Change] Rare mutations QC rule now uses reversion and labeled mutation counts (Nextclade) -Reversions and labeled mutations (see feature above) are particularly common in contaminated samples, coinfections and recombination. To draw the user's attention to such sequences, both types of private mutation now get higher weights private mutation QC rule. +Reversions and labeled mutations (see feature above) are particularly common in contaminated samples, coinfections and recombination. To draw the user's attention to such sequences, both types of private mutation now get higher weights in the private mutation QC rule. ## Nextclade Web 1.12.0, Nextclade CLI 1.9.0, Nextalign CLI 1.9.0 (2022-01-11) From 9b68a4e4c800b524248a7684499e2c96d61e8000 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Mon, 24 Jan 2022 19:18:34 +0100 Subject: [PATCH 07/13] chore: add fix PR #696 to CHANGELOG --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5d4c4cd29..71f2189d8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,10 @@ Nucleotide insertions are now additionally translated into amino acids. You can Reversions and labeled mutations (see feature above) are particularly common in contaminated samples, coinfections and recombination. To draw the user's attention to such sequences, both types of private mutation now get higher weights in the private mutation QC rule. +### [Fix] Gaps in query sequences are now stripped correctly [#696](https://github.com/nextstrain/nextclade/pull/696) + +When query sequences contained gaps (-), e.g. when inputting aligned sequences, gaps were not stripped correctly since v1.7.0 (web v1.10.0), which could lead to - showing up in insertions. + ## Nextclade Web 1.12.0, Nextclade CLI 1.9.0, Nextalign CLI 1.9.0 (2022-01-11) ### [Feature] Handle "-" strand gene translation From 209f9e48e599e60878803f2a40f416d15fd42ddc Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Mon, 24 Jan 2022 19:24:39 +0100 Subject: [PATCH 08/13] docs(changelog): link to stable docs --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 71f2189d8..47284b180 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,7 @@ Private mutations (differences between a query sequence and nearest neighbour in 2. (SARS-CoV-2 only for now) Mutation to a genotype common in at least 1 clade get labeled with that clade 3. Mutations that are neither reversions nor labeled (called "unlabeled") -Which category a mutation belongs to is visible by hovering over the "divergence" column (in web) and in various "privateNucMutations" fields in [csv/tsv/json outputs](https://docs.nextstrain.org/projects/nextclade/en/latest/user/output-files.html#tabular-csv-tsv-results). +Which category a mutation belongs to is visible by hovering over the "divergence" column (in web) and in various "privateNucMutations" fields in [csv/tsv/json outputs](https://docs.nextstrain.org/projects/nextclade/en/stable/user/output-files.html#tabular-csv-tsv-results). ### [Feature] Insertions now also available as amino acids [#692](https://github.com/nextstrain/nextclade/pull/692) From 5829f0849d43b9a936f36fef0e1b94e96d67d03c Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Mon, 24 Jan 2022 19:25:56 +0100 Subject: [PATCH 09/13] docs(changelog): fix column name --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 47284b180..9e1164bc5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,7 @@ Private mutations (differences between a query sequence and nearest neighbour in 2. (SARS-CoV-2 only for now) Mutation to a genotype common in at least 1 clade get labeled with that clade 3. Mutations that are neither reversions nor labeled (called "unlabeled") -Which category a mutation belongs to is visible by hovering over the "divergence" column (in web) and in various "privateNucMutations" fields in [csv/tsv/json outputs](https://docs.nextstrain.org/projects/nextclade/en/stable/user/output-files.html#tabular-csv-tsv-results). +Which category a mutation belongs to is visible by hovering over the "Mut." column in Nextclade Web and in various "privateNucMutations" fields in [csv/tsv/json outputs](https://docs.nextstrain.org/projects/nextclade/en/stable/user/output-files.html#tabular-csv-tsv-results). ### [Feature] Insertions now also available as amino acids [#692](https://github.com/nextstrain/nextclade/pull/692) From 6a55149228574bcea69a7e344500968c07ed3e4f Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Mon, 24 Jan 2022 19:30:48 +0100 Subject: [PATCH 10/13] docs(changelog): reword paragraph about aa insertions To deemphasize that they are translated from nucs. They are, but then there's also alignment and many other things happen. --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9e1164bc5..454952ac8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ Which category a mutation belongs to is visible by hovering over the "Mut." colu ### [Feature] Insertions now also available as amino acids [#692](https://github.com/nextstrain/nextclade/pull/692) -Nucleotide insertions are now additionally translated into amino acids. You can find them by hovering over the "insertions" column in the web app and as "aaInsertions" and "totalAminoacidInsertions" fields in Nextalign and Nextclade output. +Aminoacid insertions relative to the reference peptide are now display in the over the "Ins." column in Nextclade Web and are emitted as "aaInsertions" and "totalAminoacidInsertions" fields in Nextalign and Nextclade output files. Note, that similarly to nucleotide insertions, aminoacid insertions are stripped from the output alignment. ### [Change] Rare mutations QC rule now uses reversion and labeled mutation counts (Nextclade) From 03b5f5d696470341ae9deed5194dbe7bef3052e2 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Mon, 24 Jan 2022 19:37:12 +0100 Subject: [PATCH 11/13] docs(changelog): reword paragraph about private mutations qc --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 454952ac8..631c00747 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,9 +14,9 @@ Which category a mutation belongs to is visible by hovering over the "Mut." colu Aminoacid insertions relative to the reference peptide are now display in the over the "Ins." column in Nextclade Web and are emitted as "aaInsertions" and "totalAminoacidInsertions" fields in Nextalign and Nextclade output files. Note, that similarly to nucleotide insertions, aminoacid insertions are stripped from the output alignment. -### [Change] Rare mutations QC rule now uses reversion and labeled mutation counts (Nextclade) +### [Change] "Private mutations" QC rule now accounts for reversions and labeled mutations -Reversions and labeled mutations (see feature above) are particularly common in contaminated samples, coinfections and recombination. To draw the user's attention to such sequences, both types of private mutation now get higher weights in the private mutation QC rule. +Reversions and labeled mutations (see feature above) are particularly common in contaminated samples, coinfections and recombination. To draw the user's attention to such sequences, both types of private mutation now get higher weights in the "Private mutations" QC rule (denoted as "P" in Nextclade Web, and `qc.privateMutations` in output files). ### [Fix] Gaps in query sequences are now stripped correctly [#696](https://github.com/nextstrain/nextclade/pull/696) From 2a2b8bd31229ae273b9f84f23f3e9cde5e3a1729 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Mon, 24 Jan 2022 19:37:58 +0100 Subject: [PATCH 12/13] docs(changelog): move paragraph about qc closer to the related feature --- CHANGELOG.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 631c00747..7fc429509 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,14 +10,14 @@ Private mutations (differences between a query sequence and nearest neighbour in Which category a mutation belongs to is visible by hovering over the "Mut." column in Nextclade Web and in various "privateNucMutations" fields in [csv/tsv/json outputs](https://docs.nextstrain.org/projects/nextclade/en/stable/user/output-files.html#tabular-csv-tsv-results). -### [Feature] Insertions now also available as amino acids [#692](https://github.com/nextstrain/nextclade/pull/692) - -Aminoacid insertions relative to the reference peptide are now display in the over the "Ins." column in Nextclade Web and are emitted as "aaInsertions" and "totalAminoacidInsertions" fields in Nextalign and Nextclade output files. Note, that similarly to nucleotide insertions, aminoacid insertions are stripped from the output alignment. - ### [Change] "Private mutations" QC rule now accounts for reversions and labeled mutations Reversions and labeled mutations (see feature above) are particularly common in contaminated samples, coinfections and recombination. To draw the user's attention to such sequences, both types of private mutation now get higher weights in the "Private mutations" QC rule (denoted as "P" in Nextclade Web, and `qc.privateMutations` in output files). +### [Feature] Insertions now also available as amino acids [#692](https://github.com/nextstrain/nextclade/pull/692) + +Aminoacid insertions relative to the reference peptide are now display in the over the "Ins." column in Nextclade Web and are emitted as "aaInsertions" and "totalAminoacidInsertions" fields in Nextalign and Nextclade output files. Note, that similarly to nucleotide insertions, aminoacid insertions are stripped from the output alignment. + ### [Fix] Gaps in query sequences are now stripped correctly [#696](https://github.com/nextstrain/nextclade/pull/696) When query sequences contained gaps (-), e.g. when inputting aligned sequences, gaps were not stripped correctly since v1.7.0 (web v1.10.0), which could lead to - showing up in insertions. From bd098d1f0f6a257f85e7a74b58d874a55035bdd1 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Mon, 24 Jan 2022 19:38:51 +0100 Subject: [PATCH 13/13] docs(changelog): fix typos --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7fc429509..494b0aa47 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ Reversions and labeled mutations (see feature above) are particularly common in ### [Feature] Insertions now also available as amino acids [#692](https://github.com/nextstrain/nextclade/pull/692) -Aminoacid insertions relative to the reference peptide are now display in the over the "Ins." column in Nextclade Web and are emitted as "aaInsertions" and "totalAminoacidInsertions" fields in Nextalign and Nextclade output files. Note, that similarly to nucleotide insertions, aminoacid insertions are stripped from the output alignment. +Aminoacid insertions in the query peptides relative to the corresponding reference peptide are now displayed in the "Ins." column in Nextclade Web and are emitted as "aaInsertions" and "totalAminoacidInsertions" fields in Nextalign and Nextclade output files. Note, that similarly to nucleotide insertions, aminoacid insertions are stripped from the output alignment. ### [Fix] Gaps in query sequences are now stripped correctly [#696](https://github.com/nextstrain/nextclade/pull/696)