[update docs] v1.3.3

GMOD · Aug 2, 2021 · ece4b32 · ece4b32
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Showing 28 changed files with 91 additions and 91 deletions.
diff --git a/lerna.json b/lerna.json
@@ -1,5 +1,5 @@
 {
-  "version": "1.3.2",
+  "version": "1.3.3",
   "npmClient": "yarn",
   "useWorkspaces": true
 }
diff --git a/packages/core/package.json b/packages/core/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "1.3.2",
+  "version": "1.3.3",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",

diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",

diff --git a/plugins/breakpoint-split-view/package.json b/plugins/breakpoint-split-view/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-breakpoint-split-view",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 breakpoint detail split view",
   "keywords": [
     "jbrowse",

diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-circular-view",
-  "version": "1.3.2",
+  "version": "1.3.3",
   "description": "JBrowse 2 circular view",
   "keywords": [
     "jbrowse",

diff --git a/plugins/config/package.json b/plugins/config/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 config utilities",
   "keywords": [
     "jbrowse",

diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",

diff --git a/plugins/dotplot-view/package.json b/plugins/dotplot-view/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-dotplot-view",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 dotplot view",
   "keywords": [
     "jbrowse",

diff --git a/plugins/filtering/package.json b/plugins/filtering/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-filtering",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 filtering tracks, etc.",
   "keywords": [
     "jbrowse",

diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "1.3.0",
+  "version": "1.3.3",
   "description": "JBrowse 2 gff3.",
   "keywords": [
     "jbrowse",

diff --git a/plugins/hic/package.json b/plugins/hic/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-hic",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 hic adapters, tracks, etc.",
   "keywords": [
     "jbrowse",

diff --git a/plugins/legacy-jbrowse/package.json b/plugins/legacy-jbrowse/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",

diff --git a/plugins/linear-comparative-view/package.json b/plugins/linear-comparative-view/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",

diff --git a/plugins/linear-genome-view/package.json b/plugins/linear-genome-view/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",

diff --git a/plugins/lollipop/package.json b/plugins/lollipop/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-lollipop",
-  "version": "1.3.0",
+  "version": "1.3.3",
   "description": "JBrowse 2 plugin for lollipops",
   "keywords": [
     "jbrowse",

diff --git a/plugins/menus/package.json b/plugins/menus/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-menus",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 basic menus",
   "keywords": [
     "jbrowse",

diff --git a/plugins/sequence/package.json b/plugins/sequence/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",

diff --git a/plugins/spreadsheet-view/package.json b/plugins/spreadsheet-view/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-spreadsheet-view",
-  "version": "1.3.2",
+  "version": "1.3.3",
   "description": "JBrowse 2 spreadsheet view",
   "keywords": [
     "jbrowse",
@@ -37,7 +37,7 @@
   "dependencies": {
     "@gmod/bgzf-filehandle": "^1.3.4",
     "@gmod/vcf": "^4.0.0",
-    "@jbrowse/plugin-variants": "^1.3.2",
+    "@jbrowse/plugin-variants": "^1.3.3",
     "@material-ui/icons": "^4.9.1",
     "classnames": "^2.2.6",
     "csvtojson": "^2.0.10"

diff --git a/plugins/sv-inspector/package.json b/plugins/sv-inspector/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sv-inspector",
-  "version": "1.3.2",
+  "version": "1.3.3",
   "description": "JBrowse 2 SV inspector view",
   "keywords": [
     "jbrowse",

diff --git a/plugins/svg/package.json b/plugins/svg/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-svg",
-  "version": "1.3.2",
+  "version": "1.3.3",
   "description": "JBrowse 2 plugin for svg features",
   "keywords": [
     "jbrowse",

diff --git a/plugins/trackhub-registry/package.json b/plugins/trackhub-registry/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-trackhub-registry",
-  "version": "1.3.0",
+  "version": "1.3.3",
   "description": "Add a connection to The Track Hub Registry",
   "keywords": [
     "jbrowse",

diff --git a/plugins/variants/package.json b/plugins/variants/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "1.3.2",
+  "version": "1.3.3",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",

diff --git a/plugins/wiggle/package.json b/plugins/wiggle/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",

diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md
@@ -134,7 +134,7 @@ EXAMPLES
   $ jbrowse add-assembly GRCh38.fa --target /path/to/jb2/installation/customconfig.json --load copy
 ```
 
-_See code: [src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/add-assembly.ts)_
+_See code: [src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.3/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -188,7 +188,7 @@ EXAMPLES
   /path/to/jb2/installation/config.json
 ```
 
-_See code: [src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/add-connection.ts)_
+_See code: [src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.3/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -262,7 +262,7 @@ EXAMPLES
   $ jbrowse add-track /url/relative/path.bam --trackId AlignmentsTrack1 --load url --overwrite
 ```
 
-_See code: [src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/add-track.ts)_
+_See code: [src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.3/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -287,7 +287,7 @@ EXAMPLES
   $ jbrowse add-track-json track.json --update
 ```
 
-_See code: [src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/add-track-json.ts)_
+_See code: [src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.3/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -315,7 +315,7 @@ EXAMPLES
   $ jbrowse admin-server -p 8888
 ```
 
-_See code: [src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/admin-server.ts)_
+_See code: [src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.3/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -350,7 +350,7 @@ EXAMPLES
   $ jbrowse create --listVersions # Lists out all available versions of JBrowse 2
 ```
 
-_See code: [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/create.ts)_
+_See code: [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.3/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMAND]`
 
@@ -404,7 +404,7 @@ EXAMPLES
   $ jbrowse set-default-session --currentSession # Prints out current default session
 ```
 
-_See code: [src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/set-default-session.ts)_
+_See code: [src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.3/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -438,7 +438,7 @@ EXAMPLES
   $ jbrowse upgrade --url https://sample.com/jbrowse2.zip
 ```
 
-_See code: [src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/upgrade.ts)_
+_See code: [src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.3/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

diff --git a/products/jbrowse-cli/package.json b/products/jbrowse-cli/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "1.3.2",
+  "version": "1.3.3",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",

diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/desktop",
-  "version": "1.3.2",
+  "version": "1.3.3",
   "description": "JBrowse desktop application specialized to inspect structural variants",
   "license": "Apache-2.0",
   "homepage": "./",
@@ -36,30 +36,30 @@
     "build-electron-only-unpacked:linux": "electron-builder build -l --dir"
   },
   "dependencies": {
-    "@jbrowse/core": "^1.3.2",
-    "@jbrowse/plugin-alignments": "^1.3.1",
+    "@jbrowse/core": "^1.3.3",
+    "@jbrowse/plugin-alignments": "^1.3.3",
     "@jbrowse/plugin-bed": "^1.3.1",
-    "@jbrowse/plugin-breakpoint-split-view": "^1.3.1",
-    "@jbrowse/plugin-circular-view": "^1.3.2",
-    "@jbrowse/plugin-config": "^1.3.1",
-    "@jbrowse/plugin-data-management": "^1.3.1",
-    "@jbrowse/plugin-dotplot-view": "^1.3.1",
-    "@jbrowse/plugin-filtering": "^1.3.1",
-    "@jbrowse/plugin-gff3": "^1.3.0",
-    "@jbrowse/plugin-hic": "^1.3.1",
-    "@jbrowse/plugin-legacy-jbrowse": "^1.3.1",
-    "@jbrowse/plugin-linear-comparative-view": "^1.3.1",
-    "@jbrowse/plugin-linear-genome-view": "^1.3.1",
-    "@jbrowse/plugin-lollipop": "^1.3.0",
-    "@jbrowse/plugin-menus": "^1.3.1",
+    "@jbrowse/plugin-breakpoint-split-view": "^1.3.3",
+    "@jbrowse/plugin-circular-view": "^1.3.3",
+    "@jbrowse/plugin-config": "^1.3.3",
+    "@jbrowse/plugin-data-management": "^1.3.3",
+    "@jbrowse/plugin-dotplot-view": "^1.3.3",
+    "@jbrowse/plugin-filtering": "^1.3.3",
+    "@jbrowse/plugin-gff3": "^1.3.3",
+    "@jbrowse/plugin-hic": "^1.3.3",
+    "@jbrowse/plugin-legacy-jbrowse": "^1.3.3",
+    "@jbrowse/plugin-linear-comparative-view": "^1.3.3",
+    "@jbrowse/plugin-linear-genome-view": "^1.3.3",
+    "@jbrowse/plugin-lollipop": "^1.3.3",
+    "@jbrowse/plugin-menus": "^1.3.3",
     "@jbrowse/plugin-rdf": "^1.3.1",
-    "@jbrowse/plugin-sequence": "^1.3.1",
-    "@jbrowse/plugin-spreadsheet-view": "^1.3.2",
-    "@jbrowse/plugin-sv-inspector": "^1.3.2",
-    "@jbrowse/plugin-svg": "^1.3.2",
-    "@jbrowse/plugin-trackhub-registry": "^1.3.0",
-    "@jbrowse/plugin-variants": "^1.3.2",
-    "@jbrowse/plugin-wiggle": "^1.3.1",
+    "@jbrowse/plugin-sequence": "^1.3.3",
+    "@jbrowse/plugin-spreadsheet-view": "^1.3.3",
+    "@jbrowse/plugin-sv-inspector": "^1.3.3",
+    "@jbrowse/plugin-svg": "^1.3.3",
+    "@jbrowse/plugin-trackhub-registry": "^1.3.3",
+    "@jbrowse/plugin-variants": "^1.3.3",
+    "@jbrowse/plugin-wiggle": "^1.3.3",
     "@librpc/web": "rbuels/librpc-web#737bb9706762a52a87169a12c9b59fb241febab0",
     "@material-ui/core": "^4.12.2",
     "@material-ui/data-grid": "^4.0.0-alpha.34",

diff --git a/products/jbrowse-react-linear-genome-view/package.json b/products/jbrowse-react-linear-genome-view/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/react-linear-genome-view",
-  "version": "1.3.2",
+  "version": "1.3.3",
   "description": "JBrowse 2 linear genome view React component",
   "keywords": [
     "jbrowse",
@@ -33,18 +33,18 @@
     "build:storybook": "build-storybook --quiet --static-dir public"
   },
   "dependencies": {
-    "@jbrowse/core": "^1.3.2",
-    "@jbrowse/plugin-alignments": "^1.3.1",
+    "@jbrowse/core": "^1.3.3",
+    "@jbrowse/plugin-alignments": "^1.3.3",
     "@jbrowse/plugin-bed": "^1.3.1",
-    "@jbrowse/plugin-circular-view": "^1.3.2",
-    "@jbrowse/plugin-config": "^1.3.1",
-    "@jbrowse/plugin-data-management": "^1.3.1",
-    "@jbrowse/plugin-gff3": "^1.3.0",
-    "@jbrowse/plugin-linear-genome-view": "^1.3.1",
-    "@jbrowse/plugin-sequence": "^1.3.1",
-    "@jbrowse/plugin-svg": "^1.3.2",
-    "@jbrowse/plugin-variants": "^1.3.2",
-    "@jbrowse/plugin-wiggle": "^1.3.1",
+    "@jbrowse/plugin-circular-view": "^1.3.3",
+    "@jbrowse/plugin-config": "^1.3.3",
+    "@jbrowse/plugin-data-management": "^1.3.3",
+    "@jbrowse/plugin-gff3": "^1.3.3",
+    "@jbrowse/plugin-linear-genome-view": "^1.3.3",
+    "@jbrowse/plugin-sequence": "^1.3.3",
+    "@jbrowse/plugin-svg": "^1.3.3",
+    "@jbrowse/plugin-variants": "^1.3.3",
+    "@jbrowse/plugin-wiggle": "^1.3.3",
     "@material-ui/core": "^4.12.2",
     "@material-ui/icons": "^4.0.0",
     "@material-ui/lab": "^4.0.0-alpha.45",