@genome-spy/app 0.90.0 → 1.1.0

package/dist/schema.json

@@ -17894,6 +17894,13 @@
           "$ref": "#/definitions/IndexUrlSourceRef",
           "description": "URL of the index file. When `url` is a template, this can be an index URL template using the same placeholder and values.\n\n__Default value:__ `url` + `\".bai\"`."
         },
+        "tags": {
+          "description": "SAM auxiliary tags to expose on each read, for example `[\"HP\", \"CB\"]`. Each tag is available as a field named `tag_` followed by the tag name, for example `tag_HP`. The field is `undefined` when a read lacks the tag. Tags that are not listed are not decoded.",
+          "items": {
+            "type": "string"
+          },
+          "type": "array"
+        },
         "type": {
           "const": "bam",
           "type": "string"

package/package.json

@@ -8,7 +8,7 @@
   "contributors": [],
   "license": "MIT",
   "homepage": "https://genomespy.app/",
-  "version": "0.90.0",
+  "version": "1.1.0",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "type": "module",
@@ -51,7 +51,7 @@
   ],
   "repository": {
     "type": "git",
-    "url": "github:genome-spy/genome-spy",
+    "url": "git+https://github.com/genome-spy/genome-spy.git",
     "directory": "packages/app"
   },
   "scripts": {
@@ -63,15 +63,14 @@
     "test:tsc:tests": "tsc -p tsconfig.tests.json --noEmit",
     "smoke:examples:webgpu": "node ../core/scripts/runWebGpuExamples.mjs --scope app --all --compare-webgl",
     "storybook": "storybook dev -p 6006",
-    "build-storybook": "storybook build",
-    "prepublishOnly": "npm run build"
+    "build-storybook": "storybook build"
   },
   "dependencies": {
     "@floating-ui/dom": "^1.6.1",
     "@fortawesome/fontawesome-free": "^6.4.2",
     "@fortawesome/fontawesome-svg-core": "^6.4.2",
     "@fortawesome/free-solid-svg-icons": "^6.4.2",
-    "@genome-spy/core": "^0.90.0",
+    "@genome-spy/core": "^1.1.0",
     "@reduxjs/toolkit": "^2.11.0",
     "d3-color": "^3.1.0",
     "idb": "^7.1.1",
@@ -84,8 +83,7 @@
     "zarrita": "^0.6.1"
   },
   "devDependencies": {
-    "@genome-spy/app-agent": "^0.90.0",
-    "@genome-spy/inspector": "^0.90.0"
-  },
-  "gitHead": "9c73e2cc6f8f3b5146c29ac69a9ae46fcc6d09a3"
+    "@genome-spy/app-agent": "^1.1.0",
+    "@genome-spy/inspector": "^1.1.0"
+  }
 }

package/LICENSE

@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2018-2026 Kari Lavikka
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

package/dist/AbortablePromiseCache-BTmAcN-t.js

@@ -1,96 +0,0 @@
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-	}
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package/dist/esm-BiqrFjMh.js

@@ -1,443 +0,0 @@
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-	return {
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-		uncompressed: a
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-}
-function s(e, t) {
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-		let i = n + r >>> 1;
-		e[i] <= t ? n = i + 1 : r = i;
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-	return n;
-}
-var c = class {
-	filehandle;
-	index;
-	constructor({ filehandle: e }) {
-		this.filehandle = e;
-	}
-	_getIndex() {
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-			throw this.index = void 0, e;
-		}), this.index;
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-			n.push(e);
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-	return r;
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-		if (n.length < 5) throw Error(`Malformed FAI line (expected 5 tab-separated columns, got ${String(n.length)}): ${t}`);
-		let [i, a, o, s, c] = n;
-		if (i.startsWith(">")) throw Error("found > in sequence name, might have supplied FASTA file for the FASTA index");
-		let l = +a, u = +s;
-		if (l > 0 && u === 0) throw Error(`Invalid FAI index for "${i}": LINEBASES is 0, FASTA likely missing trailing newline; regenerate the .fai index`);
-		r.set(i, {
-			length: l,
-			offset: +o,
-			lineLength: u,
-			lineBytes: +c
-		});
-	}
-	return r;
-}
-async function T(e, t, n = 0, r, i) {
-	if (n < 0) throw TypeError("regionStart cannot be less than 0");
-	let a = Math.min(r ?? t.length, t.length);
-	if (n >= a) return "";
-	let o = C(t.offset, t.lineBytes, t.lineLength, n), s = C(t.offset, t.lineBytes, t.lineLength, a) - o, c = S.decode(await e.read(s, o, i)).replace(/\s+/g, "");
-	if (/[^\x20-\x7e]/.test(c.slice(0, 1e3))) throw Error("Non-ASCII bytes in sequence; file may be gzip — use BgzipIndexedFasta or decompress");
-	return c;
-}
-var E = class {
-	fasta;
-	fai;
-	indexCache = new x({});
-	constructor({ fasta: e, fai: t, path: r, faiPath: i }) {
-		if (e) this.fasta = e;
-		else if (r) this.fasta = new n(r);
-		else throw Error("Need to pass filehandle for fasta or path to localfile");
-		if (t) this.fai = t;
-		else if (i) this.fai = new n(i);
-		else if (r) this.fai = new n(`${r}.fai`);
-		else throw Error("Need to pass filehandle for fai or path to localfile");
-	}
-	getIndexes(e) {
-		return this.indexCache.get("fai", e?.signal, (t) => w(this.fai, {
-			...e,
-			signal: t
-		}));
-	}
-	async getSequenceNames(e) {
-		return [...(await this.getIndexes(e)).keys()];
-	}
-	async getSequenceSizes(e) {
-		let t = {};
-		for (let [n, r] of await this.getIndexes(e)) t[n] = r.length;
-		return t;
-	}
-	async getSequenceSize(e, t) {
-		return (await this.getIndexes(t)).get(e)?.length;
-	}
-	async hasReferenceSequence(e, t) {
-		return (await this.getIndexes(t)).has(e);
-	}
-	async getResiduesByName(e, t, n, r) {
-		let i = (await this.getIndexes(r)).get(e);
-		if (i !== void 0) return T(this.fasta, i, t, n, r);
-	}
-	async getSequence(e, t, n, r) {
-		return this.getResiduesByName(e, t, n, r);
-	}
-}, D = class extends E {
-	constructor({ fasta: e, path: t, fai: r, faiPath: i, gzi: a, gziPath: o }) {
-		let s;
-		if (e && a) s = new m({
-			filehandle: e,
-			gziFilehandle: a
-		});
-		else if (t && o) s = new m({
-			filehandle: new n(t),
-			gziFilehandle: new n(o)
-		});
-		else throw Error("BgzipIndexedFasta requires either {fasta, gzi} or {path, gziPath}");
-		super({
-			fasta: s,
-			fai: r,
-			faiPath: i,
-			path: t
-		});
-	}
-};
-//#endregion
-export { D as BgzipIndexedFasta, _ as FetchableSmallFasta, E as IndexedFasta, g as parseSmallFasta };