@jbrowse/cli 2.12.0 → 2.12.2

package/README.md

@@ -205,7 +205,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.2/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -256,7 +256,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.2/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -337,7 +337,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.2/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -367,7 +367,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.2/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -399,7 +399,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.2/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -456,7 +456,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.2/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMAND]`
 
@@ -507,7 +507,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/make-pif.ts)_
+[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.2/products/jbrowse-cli/src/commands/make-pif.ts)_
 
 ## `jbrowse remove-track TRACK`
 
@@ -535,7 +535,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.2/products/jbrowse-cli/src/commands/remove-track.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -577,7 +577,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.2/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse sort-gff FILE`
 
@@ -608,7 +608,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/sort-gff.ts)_
+[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.2/products/jbrowse-cli/src/commands/sort-gff.ts)_
 
 ## `jbrowse text-index`
 
@@ -675,7 +675,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.2/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -738,7 +738,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.0/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.2/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/commands/make-pif.js

@@ -3,7 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createPIF = exports.swapIndelCigar = exports.flipCigar = void 0;
+exports.flipCigar = flipCigar;
+exports.swapIndelCigar = swapIndelCigar;
+exports.createPIF = createPIF;
 const fs_1 = __importDefault(require("fs"));
 const readline_1 = __importDefault(require("readline"));
 const zlib_1 = require("zlib");
@@ -44,11 +46,9 @@ function flipCigar(cigar) {
     }
     return arr;
 }
-exports.flipCigar = flipCigar;
 function swapIndelCigar(cigar) {
     return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I');
 }
-exports.swapIndelCigar = swapIndelCigar;
 async function createPIF(filename, stream) {
     const rl1 = filename ? getReadline(filename) : getStdReadline();
     for await (const line of rl1) {
@@ -65,7 +65,6 @@ async function createPIF(filename, stream) {
     }
     rl1.close();
 }
-exports.createPIF = createPIF;
 class MakePIF extends base_1.default {
     async run() {
         const { args: { file }, flags: { out, csi }, } = await this.parse(MakePIF);

package/lib/fetchWithProxy.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = fetchWithProxy;
 const node_1 = require("node-fetch-native/node");
 const proxy_1 = require("node-fetch-native/proxy");
 const proxy = (0, proxy_1.createProxy)();
@@ -9,4 +10,3 @@ const proxy = (0, proxy_1.createProxy)();
 function fetchWithProxy(url, options = {}) {
     return (0, node_1.fetch)(url, { ...options, ...proxy });
 }
-exports.default = fetchWithProxy;

package/lib/types/common.js

@@ -3,7 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.generateMeta = exports.supported = exports.guessAdapterFromFileName = exports.isURL = exports.createRemoteStream = void 0;
+exports.createRemoteStream = createRemoteStream;
+exports.isURL = isURL;
+exports.guessAdapterFromFileName = guessAdapterFromFileName;
+exports.supported = supported;
+exports.generateMeta = generateMeta;
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
@@ -14,7 +18,6 @@ async function createRemoteStream(urlIn) {
     }
     return response;
 }
-exports.createRemoteStream = createRemoteStream;
 function isURL(FileName) {
     let url;
     try {
@@ -25,7 +28,6 @@ function isURL(FileName) {
     }
     return url.protocol === 'http:' || url.protocol === 'https:';
 }
-exports.isURL = isURL;
 function makeLocation(location, protocol) {
     if (protocol === 'uri') {
         return {
@@ -104,7 +106,6 @@ function guessAdapterFromFileName(filePath) {
         throw new Error(`Unsupported file type ${filePath}`);
     }
 }
-exports.guessAdapterFromFileName = guessAdapterFromFileName;
 function supported(type) {
     return [
         'Gff3TabixAdapter',
@@ -113,7 +114,6 @@ function supported(type) {
         'VcfAdapter',
     ].includes(type);
 }
-exports.supported = supported;
 async function generateMeta({ trackConfigs, attributes, outLocation, name, typesToExclude, assemblyNames, }) {
     const tracks = trackConfigs.map(({ adapter, textSearching, trackId }) => ({
         trackId,
@@ -127,4 +127,3 @@ async function generateMeta({ trackConfigs, attributes, outLocation, name, types
         assemblyNames,
     }, null, 2));
 }
-exports.generateMeta = generateMeta;

package/lib/types/gff3Adapter.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexGff3 = void 0;
+exports.indexGff3 = indexGff3;
 const cli_progress_1 = require("cli-progress");
 const zlib_1 = require("zlib");
 const readline_1 = __importDefault(require("readline"));
@@ -69,4 +69,3 @@ async function* indexGff3({ config, attributesToIndex, inLocation, outLocation,
     }
     progressBar.stop();
 }
-exports.indexGff3 = indexGff3;

package/lib/types/vcfAdapter.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexVcf = void 0;
+exports.indexVcf = indexVcf;
 const cli_progress_1 = require("cli-progress");
 const zlib_1 = require("zlib");
 const readline_1 = __importDefault(require("readline"));
@@ -74,4 +74,3 @@ async function* indexVcf({ config, attributesToIndex, inLocation, outLocation, q
     }
     progressBar.stop();
 }
-exports.indexVcf = indexVcf;

package/lib/util.js

@@ -3,7 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.decodeURIComponentNoThrow = exports.getLocalOrRemoteStream = void 0;
+exports.getLocalOrRemoteStream = getLocalOrRemoteStream;
+exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;
 const common_1 = require("./types/common");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
@@ -22,7 +23,6 @@ async function getLocalOrRemoteStream(uri, out) {
     }
     return { totalBytes, stream };
 }
-exports.getLocalOrRemoteStream = getLocalOrRemoteStream;
 function decodeURIComponentNoThrow(uri) {
     try {
         return decodeURIComponent(uri);
@@ -32,4 +32,3 @@ function decodeURIComponentNoThrow(uri) {
         return uri;
     }
 }
-exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;

package/oclif.manifest.json

@@ -1127,5 +1127,5 @@
       ]
     }
   },
-  "version": "2.12.0"
+  "version": "2.12.2"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "2.12.0",
+  "version": "2.12.2",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -74,5 +74,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
+  "gitHead": "1ec66736ce048a1637f52b7a7ef2eb02d956b771"
 }