@jbrowse/img 2.2.0 → 2.2.2

package/README.md

@@ -107,10 +107,7 @@ Some jbrowse track types (alignments, gene tracks, etc) will not display if
 zoomed too far out. Add force:true to make it render
 
 ```bash
-jb2export --config data/config.json \
-  --loc 1:1,100,000-1,200,000 \
-  --assembly hg19 \
-  --configtracks hg00096_lowcov force:true
+jb2export --bam file.bam force:true --loc 1:1,100,000-1,200,000 --fasta hg19.fa
 ```
 
 ### Render the sequence track

package/dist/bin.d.ts

@@ -0,0 +1,2 @@
+#!/usr/bin/env node
+export {};

package/dist/bin.js

@@ -1,4 +1,4 @@
 #!/usr/bin/env node
 "use strict";
-
-require('./index.js');
+require('./index.js');
+//# sourceMappingURL=bin.js.map

package/dist/bin.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"bin.js","sourceRoot":"","sources":["../src/bin.js"],"names":[],"mappings":";;AACA,OAAO,CAAC,YAAY,CAAC,CAAA"}

package/dist/index.d.ts

@@ -0,0 +1 @@
+import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only';

package/dist/index.js

@@ -1,209 +1,214 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-var _typeof = require("@babel/runtime/helpers/typeof");
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-var _fs = _interopRequireDefault(require("fs"));
-var _yargs = _interopRequireDefault(require("yargs"));
-var _parseArgv = require("./parseArgv");
-var _renderRegion = require("./renderRegion");
-var _tmp = _interopRequireDefault(require("tmp"));
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const fs_1 = __importDefault(require("fs"));
+const yargs_1 = __importDefault(require("yargs"));
 require("abortcontroller-polyfill/dist/abortcontroller-polyfill-only");
-var _child_process = require("child_process");
-var _nodeFetch = _interopRequireWildcard(require("node-fetch"));
-var _jsdom = require("jsdom");
-var _canvas = require("canvas");
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-/* eslint-disable no-console */
-
-global.nodeImage = _canvas.Image;
-global.nodeCreateCanvas = _canvas.createCanvas;
-var document = new _jsdom.JSDOM("...").window.document;
+const node_fetch_1 = __importStar(require("node-fetch"));
+const jsdom_1 = require("jsdom");
+const canvas_1 = require("canvas");
+// locals
+const parseArgv_1 = require("./parseArgv");
+const renderRegion_1 = require("./renderRegion");
+const util_1 = require("./util");
+// @ts-ignore
+global.nodeImage = canvas_1.Image;
+// @ts-ignore
+global.nodeCreateCanvas = canvas_1.createCanvas;
+const { document } = new jsdom_1.JSDOM(`...`).window;
 global.document = document;
-if (!global.fetch) {
-  global.fetch = _nodeFetch.default;
-  global.Headers = _nodeFetch.Headers;
-  global.Response = _nodeFetch.Response;
-  global.Request = _nodeFetch.Request;
-}
-var err = console.error;
-console.error = function () {
-  for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-    args[_key] = arguments[_key];
-  }
-  if ("".concat(args[0]).match('useLayoutEffect')) {
-    return null;
-  } else {
-    err(args);
-  }
+// force use of node-fetch polyfill, even if node 18+ fetch is available.
+// native node 18+ fetch currently gives errors related to unidici and
+// Uint8Array:
+//
+//
+// % node --version
+// v18.12.1
+//
+// % jb2export --fasta https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.fa --bam https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam --loc ctgA:1-1000 --out out4.svg
+// [
+//   '(node:1387934) ExperimentalWarning: The Fetch API is an experimental feature. This feature could change at any time\n' +
+//     '(Use `node --trace-warnings ...` to show where the warning was created)'
+// ]
+// [
+//   RangeError: offset is out of bounds
+//       at Uint8Array.set (<anonymous>)
+//       at Response.arrayBuffer (node:internal/deps/undici/undici:6117:23)
+//       at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
+// ]
+// @ts-ignore
+global.fetch = node_fetch_1.default;
+// @ts-ignore
+global.Headers = node_fetch_1.Headers;
+// @ts-ignore
+global.Response = node_fetch_1.Response;
+// @ts-ignore
+global.Request = node_fetch_1.Request;
+const err = console.error;
+console.error = (...p) => {
+    if (!`${p[0]}`.match('useLayoutEffect')) {
+        err(p);
+    }
 };
-console.warn = function () {
-  for (var _len2 = arguments.length, args = new Array(_len2), _key2 = 0; _key2 < _len2; _key2++) {
-    args[_key2] = arguments[_key2];
-  }
-  if ("".concat(args[0]).match('estimation reached timeout')) {
-    return null;
-  } else {
-    err(args);
-  }
+const warn = console.warn;
+console.warn = (...p) => {
+    if (!`${p[0]}`.match('estimation reached timeout')) {
+        warn(p);
+    }
 };
-
-// eslint-disable-next-line no-unused-expressions
-_yargs.default.command('jb2export', 'Creates a jbrowse 2 image snapshot').option('config', {
-  description: 'Path to config file',
-  type: 'string'
-}).option('session', {
-  description: 'Path to session file',
-  type: 'string'
-}).option('assembly', {
-  description: 'Path to an assembly configuration, or a name of an assembly in the configFile',
-  type: 'string'
-}).option('tracks', {
-  description: 'Path to tracks portion of a session',
-  type: 'string'
-}).option('loc', {
-  description: 'A locstring to navigate to, or --loc all to view the whole genome',
-  type: 'string'
-}).option('fasta', {
-  description: 'Supply a fasta for the assembly',
-  type: 'string'
-}).option('aliases', {
-  description: 'Supply aliases for the assembly, e.g. mapping of 1 to chr1. Tab separated file where column 1 matches the names from the FASTA',
-  type: 'string'
-}).option('width', {
-  description: 'Set the width of the window that jbrowse renders to, default: 1500px',
-  type: 'number'
-}).option('pngwidth', {
-  description: 'Set the width of the png canvas if using png output, default 2048px',
-  type: 'number',
-  default: 2048
-})
-// track types
-.option('configtracks', {
-  description: 'A list of track labels from a config file',
-  type: 'array'
-}).option('bam', {
-  description: 'A bam file, flag --bam can be used multiple times to specify multiple bam files',
-  type: 'array'
-}).option('bigwig', {
-  description: 'A bigwig file, the --bigwig flag can be used multiple times to specify multiple bigwig files',
-  type: 'array'
-}).option('cram', {
-  description: 'A cram file, the --cram flag can be used multiple times to specify multiple cram files',
-  type: 'array'
-}).option('vcfgz', {
-  description: 'A tabixed VCF, the --vcfgz flag can be used multiple times to specify multiple vcfgz files',
-  type: 'array'
-}).option('gffgz', {
-  description: 'A tabixed GFF, the --gffgz can be used multiple times to specify multiple gffgz files',
-  type: 'array'
-}).option('hic', {
-  description: 'A .hic file, the --hic can be used multiple times to specify multiple hic files',
-  type: 'array'
-}).option('bigbed', {
-  description: 'A .bigBed file, the --bigbed can be used multiple times to specify multiple bigbed files',
-  type: 'array'
-}).option('bedgz', {
-  description: 'A bed tabix file, the --bedgz can be used multiple times to specify multiple bedtabix files',
-  type: 'array'
-})
-
-// other
-.option('out', {
-  description: 'File to output to. Default: out.svg. If a filename with extension .png is supplied the program will try to automatically execute rsvg-convert to convert it to png',
-  type: 'string',
-  default: 'out.svg'
-}).option('noRasterize', {
-  description: 'Use full SVG rendering with no rasterized layers, this can substantially increase filesize',
-  type: 'boolean'
-}).option('defaultSession', {
-  description: 'Use the defaultSession from config.json',
-  type: 'boolean'
-}).help().alias('help', 'h').alias('width', 'w').argv;
-
-// prints to stderr the time it takes to execute cb
-function time(_x) {
-  return _time.apply(this, arguments);
-}
-function _time() {
-  _time = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(cb) {
-    var start, ret;
-    return _regenerator.default.wrap(function _callee2$(_context2) {
-      while (1) {
-        switch (_context2.prev = _context2.next) {
-          case 0:
-            start = +Date.now();
-            _context2.next = 3;
-            return cb();
-          case 3:
-            ret = _context2.sent;
-            console.log("Finished rendering: ".concat((+Date.now() - start) / 1000, "s"));
-            return _context2.abrupt("return", ret);
-          case 6:
-          case "end":
-            return _context2.stop();
+// note: yargs is actually unused except for printing help
+// we do custom command line parsing, see parseArgv.ts
+// eslint-disable-next-line @typescript-eslint/no-floating-promises
+yargs_1.default
+    .command('jb2export', 'Creates a jbrowse 2 image snapshot')
+    .option('config', {
+    description: 'Path to config file',
+    type: 'string',
+})
+    .option('session', {
+    description: 'Path to session file',
+    type: 'string',
+})
+    .option('assembly', {
+    description: 'Path to an assembly configuration, or a name of an assembly in the configFile',
+    type: 'string',
+})
+    .option('tracks', {
+    description: 'Path to tracks portion of a session',
+    type: 'string',
+})
+    .option('loc', {
+    description: 'A locstring to navigate to, or --loc all to view the whole genome',
+    type: 'string',
+})
+    .option('fasta', {
+    description: 'Supply a fasta for the assembly',
+    type: 'string',
+})
+    .option('aliases', {
+    description: 'Supply aliases for the assembly, e.g. mapping of 1 to chr1. Tab separated file where column 1 matches the names from the FASTA',
+    type: 'string',
+})
+    .option('width', {
+    description: 'Set the width of the window that jbrowse renders to, default: 1500px',
+    type: 'number',
+})
+    .option('pngwidth', {
+    description: 'Set the width of the png canvas if using png output, default 2048px',
+    type: 'number',
+    default: 2048,
+})
+    // track types
+    .option('configtracks', {
+    description: 'A list of track labels from a config file',
+    type: 'array',
+})
+    .option('bam', {
+    description: 'A bam file, flag --bam can be used multiple times to specify multiple bam files',
+    type: 'array',
+})
+    .option('bigwig', {
+    description: 'A bigwig file, the --bigwig flag can be used multiple times to specify multiple bigwig files',
+    type: 'array',
+})
+    .option('cram', {
+    description: 'A cram file, the --cram flag can be used multiple times to specify multiple cram files',
+    type: 'array',
+})
+    .option('vcfgz', {
+    description: 'A tabixed VCF, the --vcfgz flag can be used multiple times to specify multiple vcfgz files',
+    type: 'array',
+})
+    .option('gffgz', {
+    description: 'A tabixed GFF, the --gffgz can be used multiple times to specify multiple gffgz files',
+    type: 'array',
+})
+    .option('hic', {
+    description: 'A .hic file, the --hic can be used multiple times to specify multiple hic files',
+    type: 'array',
+})
+    .option('bigbed', {
+    description: 'A .bigBed file, the --bigbed can be used multiple times to specify multiple bigbed files',
+    type: 'array',
+})
+    .option('bedgz', {
+    description: 'A bed tabix file, the --bedgz can be used multiple times to specify multiple bedtabix files',
+    type: 'array',
+})
+    // other
+    .option('out', {
+    description: 'File to output to. Default: out.svg. If a filename with extension .png is supplied the program will try to automatically execute rsvg-convert to convert it to png',
+    type: 'string',
+    default: 'out.svg',
+})
+    .option('noRasterize', {
+    description: 'Use full SVG rendering with no rasterized layers, this can substantially increase filesize',
+    type: 'boolean',
+})
+    .option('defaultSession', {
+    description: 'Use the defaultSession from config.json',
+    type: 'boolean',
+})
+    .help()
+    .alias('help', 'h')
+    .alias('width', 'w').argv;
+const args = (0, parseArgv_1.standardizeArgv)((0, parseArgv_1.parseArgv)(process.argv.slice(2)), [
+    'bam',
+    'cram',
+    'vcfgz',
+    'hic',
+    'bigwig',
+    'bigbed',
+    'bedgz',
+    'gffgz',
+    'configtracks',
+]);
+(async () => {
+    try {
+        const result = await (0, renderRegion_1.renderRegion)(args);
+        const { out = 'out.svg', pngwidth = '2048' } = args;
+        if (out.endsWith('.png')) {
+            (0, util_1.convert)(result, { out, pngwidth });
         }
-      }
-    }, _callee2);
-  }));
-  return _time.apply(this, arguments);
-}
-var args = (0, _parseArgv.standardizeArgv)((0, _parseArgv.parseArgv)(process.argv.slice(2)), ['bam', 'cram', 'vcfgz', 'hic', 'bigwig', 'bigbed', 'bedgz', 'gffgz', 'configtracks']);
-time( /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var result, outfile, tmpobj, ls, _tmpobj, _ls;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          _context.prev = 0;
-          _context.next = 3;
-          return (0, _renderRegion.renderRegion)(args);
-        case 3:
-          result = _context.sent;
-          outfile = args.out || 'out.svg';
-          if (outfile.endsWith('.png')) {
-            tmpobj = _tmp.default.fileSync({
-              mode: 420,
-              prefix: 'prefix-',
-              postfix: '.svg'
-            });
-            _fs.default.writeFileSync(tmpobj.name, result);
-            ls = (0, _child_process.spawnSync)('rsvg-convert', ['-w', args.pngwidth || 2048, tmpobj.name, '-o', outfile]);
-            console.log("rsvg-convert stderr: ".concat(ls.stderr.toString()));
-            console.log("rsvg-convert stdout: ".concat(ls.stdout.toString()));
-            _fs.default.unlinkSync(tmpobj.name);
-          } else if (outfile.endsWith('.pdf')) {
-            _tmpobj = _tmp.default.fileSync({
-              mode: 420,
-              prefix: 'prefix-',
-              postfix: '.svg'
-            });
-            _fs.default.writeFileSync(_tmpobj.name, result);
-            _ls = (0, _child_process.spawnSync)('rsvg-convert', ['-w', args.pngwidth || 2048, _tmpobj.name, '-f', 'pdf', '-o', outfile]);
-            console.log("rsvg-convert stderr: ".concat(_ls.stderr.toString()));
-            console.log("rsvg-convert stdout: ".concat(_ls.stdout.toString()));
-            _fs.default.unlinkSync(_tmpobj.name);
-          } else {
-            _fs.default.writeFileSync(outfile, result);
-          }
-
-          // manually exit the process after done rendering because autoruns or
-          // something similar otherwise keeps the nodejs process alive xref
-          // https://github.com/GMOD/jb2export/issues/6
-          process.exit(0);
-          _context.next = 13;
-          break;
-        case 9:
-          _context.prev = 9;
-          _context.t0 = _context["catch"](0);
-          console.error(_context.t0);
-          process.exit(1);
-        case 13:
-        case "end":
-          return _context.stop();
-      }
+        else if (out.endsWith('.pdf')) {
+            (0, util_1.convert)(result, { out, pngwidth }, ['-f', 'pdf']);
+        }
+        else {
+            fs_1.default.writeFileSync(out, result);
+        }
+        // manually exit the process after done rendering because autoruns or
+        // something similar otherwise keeps the nodejs process alive xref
+        // https://github.com/GMOD/jb2export/issues/6
+        process.exit(0);
+    }
+    catch (e) {
+        console.error(e);
+        process.exit(1);
     }
-  }, _callee, null, [[0, 9]]);
-})));
+})();
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,4CAAmB;AACnB,kDAAyB;AACzB,uEAAoE;AACpE,yDAA8D;AAC9D,iCAA6B;AAC7B,mCAA4C;AAE5C,SAAS;AACT,2CAAwD;AACxD,iDAAmD;AACnD,iCAAgC;AAEhC,aAAa;AACb,MAAM,CAAC,SAAS,GAAG,cAAK,CAAA;AACxB,aAAa;AACb,MAAM,CAAC,gBAAgB,GAAG,qBAAY,CAAA;AAEtC,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,aAAK,CAAC,KAAK,CAAC,CAAC,MAAM,CAAA;AAC5C,MAAM,CAAC,QAAQ,GAAG,QAAQ,CAAA;AAE1B,yEAAyE;AACzE,sEAAsE;AACtE,cAAc;AACd,EAAE;AACF,EAAE;AACF,mBAAmB;AACnB,WAAW;AACX,EAAE;AACF,+LAA+L;AAC/L,IAAI;AACJ,8HAA8H;AAC9H,gFAAgF;AAChF,IAAI;AACJ,IAAI;AACJ,wCAAwC;AACxC,wCAAwC;AACxC,2EAA2E;AAC3E,sFAAsF;AACtF,IAAI;AAEJ,aAAa;AACb,MAAM,CAAC,KAAK,GAAG,oBAAK,CAAA;AACpB,aAAa;AACb,MAAM,CAAC,OAAO,GAAG,oBAAO,CAAA;AACxB,aAAa;AACb,MAAM,CAAC,QAAQ,GAAG,qBAAQ,CAAA;AAC1B,aAAa;AACb,MAAM,CAAC,OAAO,GAAG,oBAAO,CAAA;AAExB,MAAM,GAAG,GAAG,OAAO,CAAC,KAAK,CAAA;AACzB,OAAO,CAAC,KAAK,GAAG,CAAC,GAAG,CAAY,EAAE,EAAE;IAClC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,iBAAiB,CAAC,EAAE;QACvC,GAAG,CAAC,CAAC,CAAC,CAAA;KACP;AACH,CAAC,CAAA;AAED,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,CAAA;AACzB,OAAO,CAAC,IAAI,GAAG,CAAC,GAAG,CAAY,EAAE,EAAE;IACjC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,4BAA4B,CAAC,EAAE;QAClD,IAAI,CAAC,CAAC,CAAC,CAAA;KACR;AACH,CAAC,CAAA;AAED,0DAA0D;AAC1D,sDAAsD;AACtD,mEAAmE;AACnE,eAAK;KACF,OAAO,CAAC,WAAW,EAAE,oCAAoC,CAAC;KAC1D,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EAAE,qBAAqB;IAClC,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,SAAS,EAAE;IACjB,WAAW,EAAE,sBAAsB;IACnC,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,UAAU,EAAE;IAClB,WAAW,EACT,+EAA+E;IACjF,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EAAE,qCAAqC;IAClD,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,mEAAmE;IACrE,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EAAE,iCAAiC;IAC9C,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,SAAS,EAAE;IACjB,WAAW,EACT,gIAAgI;IAClI,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,sEAAsE;IACxE,IAAI,EAAE,QAAQ;CACf,CAAC;KACD,MAAM,CAAC,UAAU,EAAE;IAClB,WAAW,EACT,qEAAqE;IACvE,IAAI,EAAE,QAAQ;IACd,OAAO,EAAE,IAAI;CACd,CAAC;IACF,cAAc;KACb,MAAM,CAAC,cAAc,EAAE;IACtB,WAAW,EAAE,2CAA2C;IACxD,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,iFAAiF;IACnF,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EACT,8FAA8F;IAChG,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,MAAM,EAAE;IACd,WAAW,EACT,wFAAwF;IAC1F,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,4FAA4F;IAC9F,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,uFAAuF;IACzF,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,iFAAiF;IACnF,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,QAAQ,EAAE;IAChB,WAAW,EACT,0FAA0F;IAC5F,IAAI,EAAE,OAAO;CACd,CAAC;KACD,MAAM,CAAC,OAAO,EAAE;IACf,WAAW,EACT,6FAA6F;IAC/F,IAAI,EAAE,OAAO;CACd,CAAC;IAEF,QAAQ;KACP,MAAM,CAAC,KAAK,EAAE;IACb,WAAW,EACT,oKAAoK;IACtK,IAAI,EAAE,QAAQ;IACd,OAAO,EAAE,SAAS;CACnB,CAAC;KACD,MAAM,CAAC,aAAa,EAAE;IACrB,WAAW,EACT,4FAA4F;IAC9F,IAAI,EAAE,SAAS;CAChB,CAAC;KACD,MAAM,CAAC,gBAAgB,EAAE;IACxB,WAAW,EAAE,yCAAyC;IACtD,IAAI,EAAE,SAAS;CAChB,CAAC;KACD,IAAI,EAAE;KACN,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC;KAClB,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC,IAAI,CAAA;AAE3B,MAAM,IAAI,GAAG,IAAA,2BAAe,EAAC,IAAA,qBAAS,EAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE;IAC7D,KAAK;IACL,MAAM;IACN,OAAO;IACP,KAAK;IACL,QAAQ;IACR,QAAQ;IACR,OAAO;IACP,OAAO;IACP,cAAc;CACf,CAAC,CAGD;AAAA,CAAC,KAAK,IAAI,EAAE;IACX,IAAI;QACF,MAAM,MAAM,GAAG,MAAM,IAAA,2BAAY,EAAC,IAAY,CAAC,CAAA;QAC/C,MAAM,EAAE,GAAG,GAAG,SAAS,EAAE,QAAQ,GAAG,MAAM,EAAE,GAAG,IAAI,CAAA;QACnD,IAAI,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE;YACxB,IAAA,cAAO,EAAC,MAAM,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,CAAA;SACnC;aAAM,IAAI,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE;YAC/B,IAAA,cAAO,EAAC,MAAM,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC,CAAA;SAClD;aAAM;YACL,YAAE,CAAC,aAAa,CAAC,GAAG,EAAE,MAAM,CAAC,CAAA;SAC9B;QAED,qEAAqE;QACrE,kEAAkE;QAClE,6CAA6C;QAC7C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;KAChB;IAAC,OAAO,CAAC,EAAE;QACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAChB,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;KAChB;AACH,CAAC,CAAC,EAAE,CAAA"}

package/dist/parseArgv.d.ts

@@ -0,0 +1,8 @@
+export type Entry = [string, string[]];
+export declare function parseArgv(argv: string[]): Entry[];
+export declare function standardizeArgv(args: Entry[], trackTypes: string[]): {
+    [key: string]: unknown;
+    trackList: Entry[];
+    out?: string | undefined;
+    pngwidth?: string | undefined;
+};

package/dist/parseArgv.js

@@ -1,38 +1,47 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.parseArgv = parseArgv;
-exports.standardizeArgv = standardizeArgv;
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.standardizeArgv = exports.parseArgv = void 0;
+// example (see parseArgv.test.js):
+// const args =
+//   '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam --defaultSession --out out.svg --noRasterize'
+//
+// expect(parseArgv(args.split(' '))).toEqual([
+//   ['bam', ['dad.bam', 'color:red']],
+//   ['vcf', ['variants.vcf']],
+//   ['bam', ['mom.bam']],
+//   ['defaultSession', []],
+//   ['out', ['out.svg']],
+//   ['noRasterize', []],
+// ])
 function parseArgv(argv) {
-  var map = [];
-  while (argv.length) {
-    var val = argv[0].slice(2);
-    argv = argv.slice(1);
-    var next = argv.findIndex(function (arg) {
-      return arg.startsWith('-');
-    });
-    if (next !== -1) {
-      map.push([val, argv.slice(0, next)]);
-      argv = argv.slice(next);
-    } else {
-      map.push([val, argv]);
-      break;
+    const map = [];
+    while (argv.length) {
+        const val = argv[0].slice(2);
+        argv = argv.slice(1);
+        const next = argv.findIndex(arg => arg.startsWith('-'));
+        if (next !== -1) {
+            map.push([val, argv.slice(0, next)]);
+            argv = argv.slice(next);
+        }
+        else {
+            map.push([val, argv]);
+            break;
+        }
     }
-  }
-  return map;
+    return map;
 }
+exports.parseArgv = parseArgv;
 function standardizeArgv(args, trackTypes) {
-  var result = {
-    trackList: []
-  };
-  args.forEach(function (arg) {
-    if (trackTypes.includes(arg[0])) {
-      result.trackList.push(arg);
-    } else {
-      result[arg[0]] = arg[1][0] || true;
-    }
-  });
-  return result;
-}
+    const result = { trackList: [] };
+    args.forEach(arg => {
+        if (trackTypes.includes(arg[0])) {
+            result.trackList.push(arg);
+        }
+        else {
+            result[arg[0]] = arg[1][0] || true;
+        }
+    });
+    return result;
+}
+exports.standardizeArgv = standardizeArgv;
+//# sourceMappingURL=parseArgv.js.map

package/dist/parseArgv.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"parseArgv.js","sourceRoot":"","sources":["../src/parseArgv.ts"],"names":[],"mappings":";;;AAEA,mCAAmC;AACnC,eAAe;AACf,4GAA4G;AAC5G,EAAE;AACF,+CAA+C;AAC/C,uCAAuC;AACvC,+BAA+B;AAC/B,0BAA0B;AAC1B,4BAA4B;AAC5B,0BAA0B;AAC1B,yBAAyB;AACzB,KAAK;AACL,SAAgB,SAAS,CAAC,IAAc;IACtC,MAAM,GAAG,GAAG,EAAa,CAAA;IACzB,OAAO,IAAI,CAAC,MAAM,EAAE;QAClB,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAC5B,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QACpB,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAA;QAEvD,IAAI,IAAI,KAAK,CAAC,CAAC,EAAE;YACf,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAA;YACpC,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;SACxB;aAAM;YACL,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CAAA;YACrB,MAAK;SACN;KACF;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAhBD,8BAgBC;AAED,SAAgB,eAAe,CAAC,IAAa,EAAE,UAAoB;IACjE,MAAM,MAAM,GAAG,EAAE,SAAS,EAAE,EAAE,EAK7B,CAAA;IACD,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE;QACjB,IAAI,UAAU,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE;YAC/B,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;SAC3B;aAAM;YACL,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,CAAA;SACnC;IACH,CAAC,CAAC,CAAA;IACF,OAAO,MAAM,CAAA;AACf,CAAC;AAfD,0CAeC"}

package/dist/renderRegion.d.ts

@@ -0,0 +1,35 @@
+import { Entry } from './parseArgv';
+export interface Opts {
+    noRasterize?: boolean;
+    loc?: string;
+    width?: number;
+    session?: string;
+    assembly?: string;
+    config?: string;
+    fasta?: string;
+    aliases?: string;
+    cytobands?: string;
+    defaultSession?: string;
+    trackList: Entry[];
+    tracks?: string;
+}
+interface Assembly {
+    name: string;
+    sequence: Record<string, unknown>;
+    refNameAliases?: Record<string, unknown>;
+    cytobands?: Record<string, unknown>;
+}
+interface Track {
+    trackId: string;
+    [key: string]: unknown;
+}
+interface Config {
+    assemblies: Assembly[];
+    assembly: Assembly;
+    tracks: Track[];
+    [key: string]: unknown;
+}
+export declare function readData({ assembly: asm, config, session, fasta, aliases, cytobands, defaultSession, tracks, trackList, }: Opts): Config;
+export declare const muiCache: import("@emotion/utils").EmotionCache;
+export declare function renderRegion(opts: Opts): Promise<string>;
+export {};