Merge pull request #210 from nextstrain/sc2-june-2024

Fix tree bug
nextstrain · Jun 13, 2024 · c5e02d4 · c5e02d4
2 parents 655cab4 + 7f54192
commit c5e02d4
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Showing 25 changed files with 20 additions and 10 deletions.
diff --git a/data/nextstrain/sars-cov-2/BA.2.86/CHANGELOG.md b/data/nextstrain/sars-cov-2/BA.2.86/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 - Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
 - All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+- Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
 
 <details>
   <summary> Newly included lineages, with designation date in parentheses</summary>

diff --git a/data/nextstrain/sars-cov-2/BA.2.86/tree.json b/data/nextstrain/sars-cov-2/BA.2.86/tree.json
diff --git a/data/nextstrain/sars-cov-2/BA.2/CHANGELOG.md b/data/nextstrain/sars-cov-2/BA.2/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 - Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
 - All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+- Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
 
 <details>
   <summary> Newly included lineages, with designation date in parentheses</summary>

diff --git a/data/nextstrain/sars-cov-2/BA.2/tree.json b/data/nextstrain/sars-cov-2/BA.2/tree.json
diff --git a/data/nextstrain/sars-cov-2/XBB/CHANGELOG.md b/data/nextstrain/sars-cov-2/XBB/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 - Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
 - All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+- Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
 
 <details>
   <summary> Newly included lineages, with designation date in parentheses</summary>

diff --git a/data/nextstrain/sars-cov-2/XBB/tree.json b/data/nextstrain/sars-cov-2/XBB/tree.json
diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/CHANGELOG.md b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 - Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
 - All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+- Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
 
 <details>
   <summary> Newly included lineages, with designation date in parentheses</summary>

diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/tree.json b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/tree.json
diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/CHANGELOG.md b/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 - Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
 - All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+- Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
 
 <details>
   <summary> Newly included lineages, with designation date in parentheses</summary>

diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/tree.json b/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/tree.json
diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/CHANGELOG.md b/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 - Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
 - All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+- Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
 
 <details>
   <summary> Newly included lineages, with designation date in parentheses</summary>

diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/dataset.zip b/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/dataset.zip
diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/tree.json b/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/tree.json
diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/CHANGELOG.md b/data_output/nextstrain/sars-cov-2/BA.2/unreleased/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 - Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
 - All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+- Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
 
 <details>
   <summary> Newly included lineages, with designation date in parentheses</summary>

diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/dataset.zip b/data_output/nextstrain/sars-cov-2/BA.2/unreleased/dataset.zip
diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/tree.json b/data_output/nextstrain/sars-cov-2/BA.2/unreleased/tree.json
diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/CHANGELOG.md b/data_output/nextstrain/sars-cov-2/XBB/unreleased/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 - Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
 - All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+- Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
 
 <details>
   <summary> Newly included lineages, with designation date in parentheses</summary>

diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/dataset.zip b/data_output/nextstrain/sars-cov-2/XBB/unreleased/dataset.zip
diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/tree.json b/data_output/nextstrain/sars-cov-2/XBB/unreleased/tree.json
diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/CHANGELOG.md b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 - Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
 - All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+- Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
 
 <details>
   <summary> Newly included lineages, with designation date in parentheses</summary>

diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/dataset.zip b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/dataset.zip
diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/tree.json b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/tree.json
diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/CHANGELOG.md b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 - Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
 - All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+- Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
 
 <details>
   <summary> Newly included lineages, with designation date in parentheses</summary>

diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/dataset.zip b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/dataset.zip
diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/tree.json b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/tree.json