@jbrowse/cli 5.0.0-beta.1 → 5.0.0-beta.10
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +149 -44
- package/dist/commands/add-track-utils/adapter-utils.js +47 -31
- package/dist/commands/add-track-utils/track-config.js +5 -7
- package/dist/commands/add-track.js +31 -9
- package/dist/commands/admin-server/index.js +13 -5
- package/dist/commands/admin-server/utils.js +8 -6
- package/dist/commands/make-density/density-generator.js +180 -0
- package/dist/commands/make-density/index.js +139 -0
- package/dist/commands/make-pif/index.js +62 -27
- package/dist/commands/make-pif/pif-generator.js +98 -132
- package/dist/commands/shared/density.js +12 -0
- package/dist/commands/text-index/adapter-utils.js +17 -7
- package/dist/commands/text-index/aggregate.js +5 -5
- package/dist/commands/text-index/command.js +3 -1
- package/dist/commands/text-index/config-utils.js +7 -7
- package/dist/commands/text-index/indexing-utils.js +21 -49
- package/dist/commands/validate/configManifest.generated.js +4064 -1845
- package/dist/commands/validate/configSchema.generated.js +20400 -0
- package/dist/commands/validate/index.js +21 -5
- package/dist/commands/validate/liftConfig.js +34 -0
- package/dist/commands/validate/markRules/aggregateFieldName.js +9 -0
- package/dist/commands/validate/markRules/autoBin.js +27 -0
- package/dist/commands/validate/markRules/colorScale.js +244 -0
- package/dist/commands/validate/markRules/cssColorsLevel4.js +162 -0
- package/dist/commands/validate/markRules/jexlStrings.js +23 -0
- package/dist/commands/validate/markRules/markProblems.js +532 -0
- package/dist/commands/validate/markRules/markRuleFacts.js +6 -0
- package/dist/commands/validate/markRules/markSpecs.js +96 -0
- package/dist/commands/validate/markRules/markVocabulary.js +57 -0
- package/dist/commands/validate/markRules/shapeNameList.js +7 -0
- package/dist/commands/validate/markRules/stepChannels.js +55 -0
- package/dist/commands/validate/schemaValidate.js +425 -0
- package/dist/commands/validate/validateConfig.js +304 -259
- package/dist/index.js +5 -0
- package/dist/version.js +1 -1
- package/package.json +6 -10
- package/bin/run +0 -4
- package/bundle/index.js +0 -1569
- package/dist/commands/make-pif/cigar-utils.js +0 -67
package/dist/index.js
CHANGED
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@@ -49,6 +49,11 @@ const registry = [
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summary: 'Creates pairwise indexed PAF (PIF), with bgzip and tabix',
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load: () => import('./commands/make-pif/index.js').then(m => m.run),
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},
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{
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name: 'make-density',
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summary: 'Counts feature starts per bin into a bigWig density sidecar, with bedGraphToBigWig',
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load: () => import('./commands/make-density/index.js').then(m => m.run),
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},
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{
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name: 'sort-gff',
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summary: 'Sort a GFF/GTF for tabix: sort -k1,1 -k4,4n, header kept on top',
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package/dist/version.js
CHANGED
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@@ -1 +1 @@
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export const version = '5.0.0-beta.
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export const version = '5.0.0-beta.10';
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package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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{
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"name": "@jbrowse/cli",
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"version": "5.0.0-beta.
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"version": "5.0.0-beta.10",
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"type": "module",
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"description": "A command line tool for working with JBrowse 2",
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"keywords": [
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@@ -21,29 +21,25 @@
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"jbrowse": "./dist/bin.js"
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},
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"files": [
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"/bin",
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"/bundle",
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"/dist"
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],
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"engines": {
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"node": ">=18.3.0"
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},
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"dependencies": {
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"ajv": "^8.20.0",
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"cli-progress": "^3.12.0",
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"ixixx": "^3.0.13",
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"serve-handler": "^6.1.7",
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"tmp": "^0.2.7",
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"@jbrowse/add-track-core": "^5.0.0-beta.
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"@jbrowse/cigar-utils": "^5.0.0-beta.
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"@jbrowse/text-indexing-core": "^5.0.0-beta.
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"@jbrowse/add-track-core": "^5.0.0-beta.10",
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"@jbrowse/cigar-utils": "^5.0.0-beta.10",
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"@jbrowse/text-indexing-core": "^5.0.0-beta.10"
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},
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"publishConfig": {
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"access": "public"
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},
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"scripts": {
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"
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"build": "tsc -p tsconfig.build.json && webpack -c webpack.config.mjs",
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"clean": "rimraf bundle",
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"build": "tsc -p tsconfig.build.json",
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"generate-readme": "./generate_readme.sh > README.md"
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}
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}
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package/bin/run
DELETED