@jbrowse/cli - npm Package Compare versions

Comparing version 2.12.0 to 2.12.1

lib/commands/make-pif.js

@@ -6,3 +6,5 @@ "use strict";
 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"));
@@ -48,7 +50,5 @@ const readline_1 = __importDefault(require("readline"));
 }
-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) {
@@ -70,3 +70,2 @@ const rl1 = filename ? getReadline(filename) : getStdReadline();
 }
-exports.createPIF = createPIF;
 class MakePIF extends base_1.default {
@@ -73,0 +72,0 @@ async run() {

lib/fetchWithProxy.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = fetchWithProxy;
 const node_1 = require("node-fetch-native/node");
@@ -12,2 +13,1 @@ const proxy_1 = require("node-fetch-native/proxy");
 }
-exports.default = fetchWithProxy;

lib/types/common.js

@@ -6,3 +6,7 @@ "use strict";
 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"));
@@ -18,3 +22,2 @@ const path_1 = __importDefault(require("path"));
 }
-exports.createRemoteStream = createRemoteStream;
 function isURL(FileName) {
@@ -30,3 +33,2 @@ let url;
 }
-exports.isURL = isURL;
 function makeLocation(location, protocol) {
@@ -110,3 +112,2 @@ if (protocol === 'uri') {
 }
-exports.guessAdapterFromFileName = guessAdapterFromFileName;
 function supported(type) {
@@ -120,3 +121,2 @@ return [
 }
-exports.supported = supported;
 async function generateMeta({ trackConfigs, attributes, outLocation, name, typesToExclude, assemblyNames, }) {
@@ -135,2 +135,1 @@ const tracks = trackConfigs.map(({ adapter, textSearching, trackId }) => ({
 }
-exports.generateMeta = generateMeta;

lib/types/gff3Adapter.js

@@ -6,3 +6,3 @@ "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexGff3 = void 0;
+exports.indexGff3 = indexGff3;
 const cli_progress_1 = require("cli-progress");
@@ -73,2 +73,1 @@ const zlib_1 = require("zlib");
 }
-exports.indexGff3 = indexGff3;

lib/types/vcfAdapter.js

@@ -6,3 +6,3 @@ "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexVcf = void 0;
+exports.indexVcf = indexVcf;
 const cli_progress_1 = require("cli-progress");
@@ -78,2 +78,1 @@ const zlib_1 = require("zlib");
 }
-exports.indexVcf = indexVcf;

lib/util.js

@@ -6,3 +6,4 @@ "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.decodeURIComponentNoThrow = exports.getLocalOrRemoteStream = void 0;
+exports.getLocalOrRemoteStream = getLocalOrRemoteStream;
+exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;
 const common_1 = require("./types/common");
@@ -26,3 +27,2 @@ const fs_1 = __importDefault(require("fs"));
 }
-exports.getLocalOrRemoteStream = getLocalOrRemoteStream;
 function decodeURIComponentNoThrow(uri) {
@@ -37,2 +37,1 @@ try {
 }
-exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;

oclif.manifest.json

@@ -1130,3 +1130,3 @@ {
   },
-  "version": "2.12.0"
+  "version": "2.12.1"
 }

package.json

 {
   "name": "@jbrowse/cli",
-  "version": "2.12.0",
+  "version": "2.12.1",
   "description": "A command line tool for working with JBrowse 2",
@@ -77,3 +77,3 @@ "keywords": [
   },
-  "gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
+  "gitHead": "20f16ae5a56ae5e4806aaa373131e540b0b5b0fd"
 }

README.md

@@ -208,3 +208,3 @@ ---
 _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/v2.12.1/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
@@ -260,3 +260,3 @@ ## `jbrowse add-connection CONNECTIONURLORPATH`
 _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/v2.12.1/products/jbrowse-cli/src/commands/add-connection.ts)_
 
@@ -342,3 +342,3 @@ ## `jbrowse add-track TRACK`
 _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/v2.12.1/products/jbrowse-cli/src/commands/add-track.ts)_
 
@@ -373,3 +373,3 @@ ## `jbrowse add-track-json TRACK`
 _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/v2.12.1/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
@@ -406,3 +406,3 @@ ## `jbrowse admin-server`
 _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/v2.12.1/products/jbrowse-cli/src/commands/admin-server.ts)_
 
@@ -464,3 +464,3 @@ ## `jbrowse create LOCALPATH`
 _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/v2.12.1/products/jbrowse-cli/src/commands/create.ts)_
 
@@ -516,3 +516,3 @@ ## `jbrowse help [COMMAND]`
 _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/v2.12.1/products/jbrowse-cli/src/commands/make-pif.ts)_
 
@@ -545,3 +545,3 @@ ## `jbrowse remove-track TRACK`
 _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/v2.12.1/products/jbrowse-cli/src/commands/remove-track.ts)_
 
@@ -588,3 +588,3 @@ ## `jbrowse set-default-session`
 _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/v2.12.1/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
@@ -620,3 +620,3 @@ ## `jbrowse sort-gff FILE`
 _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/v2.12.1/products/jbrowse-cli/src/commands/sort-gff.ts)_
 
@@ -688,3 +688,3 @@ ## `jbrowse text-index`
 _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/v2.12.1/products/jbrowse-cli/src/commands/text-index.ts)_
 
@@ -752,3 +752,3 @@ ## `jbrowse upgrade [LOCALPATH]`
 _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/v2.12.1/products/jbrowse-cli/src/commands/upgrade.ts)_
 
@@ -755,0 +755,0 @@ <!-- commandsstop -->

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Worsened metrics

Total package byte prevSize

195399

decreased by-0.17%

Lines of code

3951

decreased by-0.13%

No dependency changes