[update docs] v1.5.9

GMOD · Jan 13, 2022 · ed95a54 · ed95a54
1 parent 8c5f73e
commit ed95a54
Show file tree

Hide file tree

Showing 39 changed files with 127 additions and 127 deletions.
diff --git a/lerna.json b/lerna.json
@@ -1,5 +1,5 @@
 {
-  "version": "1.5.8",
+  "version": "1.5.9",
   "npmClient": "yarn",
   "useWorkspaces": true
 }
diff --git a/packages/core/package.json b/packages/core/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",

diff --git a/packages/development-tools/package.json b/packages/development-tools/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/development-tools",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "Tools to help with developing and building JBrowse 2 plugins",
   "keywords": [
     "jbrowse",

diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",

diff --git a/plugins/arc/package.json b/plugins/arc/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-arc",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 arc adapters, tracks, etc.",
   "keywords": [
     "jbrowse",

diff --git a/plugins/authentication/package.json b/plugins/authentication/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-authentication",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 Authentication",
   "keywords": [
     "jbrowse",
@@ -35,7 +35,7 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@jbrowse/plugin-variants": "^1.5.8",
+    "@jbrowse/plugin-variants": "^1.5.9",
     "@material-ui/icons": "^4.9.1"
   },
   "peerDependencies": {

diff --git a/plugins/bed/package.json b/plugins/bed/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 bed 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": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 dotplot view",
   "keywords": [
     "jbrowse",

diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 gff3.",
   "keywords": [
     "jbrowse",

diff --git a/plugins/grid-bookmark/package.json b/plugins/grid-bookmark/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-grid-bookmark",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 grid bookmark widget",
   "keywords": [
     "jbrowse",

diff --git a/plugins/gtf/package.json b/plugins/gtf/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",

diff --git a/plugins/hic/package.json b/plugins/hic/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-hic",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 basic menus",
   "keywords": [
     "jbrowse",

diff --git a/plugins/protein/package.json b/plugins/protein/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-protein",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 protein-specific renderers, etc.",
   "keywords": [
     "jbrowse",

diff --git a/plugins/rdf/package.json b/plugins/rdf/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-rdf",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 RDF resources",
   "keywords": [
     "jbrowse",

diff --git a/plugins/sequence/package.json b/plugins/sequence/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 spreadsheet view",
   "keywords": [
     "jbrowse",
@@ -37,7 +37,7 @@
   "dependencies": {
     "@gmod/bgzf-filehandle": "^1.4.2",
     "@gmod/vcf": "^5.0.4",
-    "@jbrowse/plugin-variants": "^1.5.8",
+    "@jbrowse/plugin-variants": "^1.5.9",
     "@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": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "description": "Add a connection to The Track Hub Registry",
   "keywords": [
     "jbrowse",

diff --git a/plugins/trix/package.json b/plugins/trix/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-trix",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 trix text search adapter",
   "keywords": [
     "jbrowse",

diff --git a/plugins/variants/package.json b/plugins/variants/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "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": "1.5.8",
+  "version": "1.5.9",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",

diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md
@@ -157,7 +157,7 @@ EXAMPLES
   $ jbrowse add-assembly myfile.fa.gz --load copy
 ```
 
-_See code: [src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.8/products/jbrowse-cli/src/commands/add-assembly.ts)_
+_See code: [src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.9/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -211,7 +211,7 @@ EXAMPLES
   /path/to/jb2/installation/config.json
 ```
 
-_See code: [src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.8/products/jbrowse-cli/src/commands/add-connection.ts)_
+_See code: [src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.9/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -285,7 +285,7 @@ EXAMPLES
   $ jbrowse add-track /url/relative/path.bam --load inPlace
 ```
 
-_See code: [src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.8/products/jbrowse-cli/src/commands/add-track.ts)_
+_See code: [src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.9/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -310,7 +310,7 @@ EXAMPLES
   $ jbrowse add-track-json track.json --update
 ```
 
-_See code: [src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.8/products/jbrowse-cli/src/commands/add-track-json.ts)_
+_See code: [src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.9/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -336,7 +336,7 @@ EXAMPLES
   $ jbrowse admin-server -p 8888
 ```
 
-_See code: [src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.8/products/jbrowse-cli/src/commands/admin-server.ts)_
+_See code: [src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.9/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -380,7 +380,7 @@ EXAMPLES
   $ jbrowse create --listVersions
 ```
 
-_See code: [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.8/products/jbrowse-cli/src/commands/create.ts)_
+_See code: [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.9/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMAND]`
 
@@ -434,7 +434,7 @@ 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/v1.5.8/products/jbrowse-cli/src/commands/set-default-session.ts)_
+_See code: [src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.9/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse text-index`
 
@@ -490,7 +490,7 @@ EXAMPLES
   $ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes
 ```
 
-_See code: [src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.8/products/jbrowse-cli/src/commands/text-index.ts)_
+_See code: [src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.9/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -536,7 +536,7 @@ EXAMPLES
   $ jbrowse upgrade --nightly
 ```
 
-_See code: [src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.8/products/jbrowse-cli/src/commands/upgrade.ts)_
+_See code: [src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.9/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": "1.5.8",
+  "version": "1.5.9",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",