@genome-spy/core 0.56.1 → 0.58.0

package/dist/bundle/remoteFile-BuaqFGWk.js

@@ -0,0 +1,94 @@
+import { b as d } from "./index-BftNdA0O.js";
+function u(n) {
+  return (typeof n == "object" && n !== null && "message" in n ? n.message : `${n}`).replace(/\.$/, "");
+}
+class $ {
+  async getBufferFromResponse(e) {
+    const t = await e.arrayBuffer();
+    return d.Buffer.from(t);
+  }
+  constructor(e, t = {}) {
+    this.baseOverrides = {}, this.url = e;
+    const r = t.fetch || globalThis.fetch.bind(globalThis);
+    if (!r)
+      throw new TypeError("no fetch function supplied, and none found in global environment");
+    t.overrides && (this.baseOverrides = t.overrides), this.fetchImplementation = r;
+  }
+  async fetch(e, t) {
+    let r;
+    try {
+      r = await this.fetchImplementation(e, t);
+    } catch (s) {
+      if (`${s}`.includes("Failed to fetch")) {
+        console.warn(`generic-filehandle: refetching ${e} to attempt to work around chrome CORS header caching bug`);
+        try {
+          r = await this.fetchImplementation(e, {
+            ...t,
+            cache: "reload"
+          });
+        } catch (i) {
+          throw new Error(`${u(i)} fetching ${e}`, { cause: i });
+        }
+      } else
+        throw new Error(`${u(s)} fetching ${e}`, { cause: s });
+    }
+    return r;
+  }
+  async read(e, t = 0, r, s = 0, i = {}) {
+    const { headers: c = {}, signal: o, overrides: f = {} } = i;
+    r < 1 / 0 ? c.range = `bytes=${s}-${s + r}` : r === 1 / 0 && s !== 0 && (c.range = `bytes=${s}-`);
+    const a = await this.fetch(this.url, {
+      ...this.baseOverrides,
+      ...f,
+      headers: {
+        ...c,
+        ...f.headers,
+        ...this.baseOverrides.headers
+      },
+      method: "GET",
+      redirect: "follow",
+      mode: "cors",
+      signal: o
+    });
+    if (!a.ok)
+      throw new Error(`HTTP ${a.status} fetching ${this.url}`);
+    if (a.status === 200 && s === 0 || a.status === 206) {
+      const l = await this.getBufferFromResponse(a), g = l.copy(e, t, 0, Math.min(r, l.length)), w = a.headers.get("content-range"), h = /\/(\d+)$/.exec(w || "");
+      return h != null && h[1] && (this._stat = { size: parseInt(h[1], 10) }), { bytesRead: g, buffer: e };
+    }
+    throw a.status === 200 ? new Error(`${this.url} fetch returned status 200, expected 206`) : new Error(`HTTP ${a.status} fetching ${this.url}`);
+  }
+  async readFile(e = {}) {
+    let t, r;
+    typeof e == "string" ? (t = e, r = {}) : (t = e.encoding, r = e, delete r.encoding);
+    const { headers: s = {}, signal: i, overrides: c = {} } = r, o = await this.fetch(this.url, {
+      headers: s,
+      method: "GET",
+      redirect: "follow",
+      mode: "cors",
+      signal: i,
+      ...this.baseOverrides,
+      ...c
+    });
+    if (o.status !== 200)
+      throw new Error(`HTTP ${o.status} fetching ${this.url}`);
+    if (t === "utf8")
+      return o.text();
+    if (t)
+      throw new Error(`unsupported encoding: ${t}`);
+    return this.getBufferFromResponse(o);
+  }
+  async stat() {
+    if (!this._stat) {
+      const e = d.Buffer.allocUnsafe(10);
+      if (await this.read(e, 0, 10, 0), !this._stat)
+        throw new Error(`unable to determine size of file at ${this.url}`);
+    }
+    return this._stat;
+  }
+  async close() {
+  }
+}
+export {
+  $ as R
+};

package/dist/schema.json

@@ -2905,6 +2905,13 @@
     "Gff3Data": {
       "additionalProperties": false,
       "properties": {
+        "addChrPrefix": {
+          "description": "Add a `chr` (boolean) or custom (string) prefix to the chromosome names in the Tabix file.\n\n__Default value:__ `false`",
+          "type": [
+            "boolean",
+            "string"
+          ]
+        },
         "channel": {
           "$ref": "#/definitions/PrimaryPositionalChannel",
           "description": "Which channel's scale domain to monitor.\n\n__Default value:__ `\"x\"`"
@@ -3654,6 +3661,9 @@
         },
         {
           "$ref": "#/definitions/Gff3Data"
+        },
+        {
+          "$ref": "#/definitions/VcfData"
         }
       ]
     },
@@ -8821,6 +8831,62 @@
       ],
       "type": "object"
     },
+    "VcfData": {
+      "additionalProperties": false,
+      "properties": {
+        "addChrPrefix": {
+          "description": "Add a `chr` (boolean) or custom (string) prefix to the chromosome names in the Tabix file.\n\n__Default value:__ `false`",
+          "type": [
+            "boolean",
+            "string"
+          ]
+        },
+        "channel": {
+          "$ref": "#/definitions/PrimaryPositionalChannel",
+          "description": "Which channel's scale domain to monitor.\n\n__Default value:__ `\"x\"`"
+        },
+        "debounce": {
+          "anyOf": [
+            {
+              "type": "number"
+            },
+            {
+              "$ref": "#/definitions/ExprRef"
+            }
+          ],
+          "description": "Debounce time for data updates, in milliseconds. Debouncing prevents excessive data updates when the user is zooming or panning around.\n\n__Default value:__ `200`"
+        },
+        "debounceMode": {
+          "description": "The debounce mode for data updates. If set to `\"domain\"`, domain change events (panning and zooming) will be debounced. If set to `\"window\"`, the data fetches initiated by the changes to the visible window (or tile) will be debounced.  If your data is small, the `\"window\"` is better as it will start fetching data while the user is still panning around, resulting in a shorter perceived latency.\n\n__Default value:__ `\"window\"`",
+          "enum": [
+            "domain",
+            "window"
+          ],
+          "type": "string"
+        },
+        "indexUrl": {
+          "description": "Url of the tabix index file.\n\n__Default value:__ `url` + `\".tbi\"`.",
+          "type": "string"
+        },
+        "type": {
+          "const": "vcf",
+          "type": "string"
+        },
+        "url": {
+          "description": "Url of the bgzip compressed file.",
+          "type": "string"
+        },
+        "windowSize": {
+          "description": "Size of each chunk when fetching the Tabix file. Data is only fetched when the length of the visible domain smaller than the window size.\n\n__Default value:__ `30000000`",
+          "type": "number"
+        }
+      },
+      "required": [
+        "type",
+        "url"
+      ],
+      "type": "object"
+    },
     "ViewBackground": {
       "additionalProperties": false,
       "properties": {

package/dist/src/data/collector.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"collector.d.ts","sourceRoot":"","sources":["../../../src/data/collector.js"],"names":[],"mappings":"AAUA;;;;;GAKG;AACH;IAkCI;;OAEG;IACH,qBAFW,OAAO,sBAAsB,EAAE,aAAa,EAetD;IAVG,qDAA2C;IAE3C,2CAA2C;IAC3C,WADW,QAAU,SAAS,KAAE,IAAI,CAAC,EAAE,CACpB;IAGnB,yFAAyF;IACzF,cADW,IAAI,OAAO,oBAAoB,EAAE,MAAM,EAAE,+BAAO,CACN;IAuHzD;;OAEG;IACH,mDAmBC;IAED;;;OAGG;IACH,6DAF6B,IAAI,QAUhC;IAED;;OAEG;IACH,uBAMC;IA8CD;;;;OAIG;IACH,8BAFW,MAAM,iCA4BhB;;CACJ;qBA/SyD,eAAe"}
+{"version":3,"file":"collector.d.ts","sourceRoot":"","sources":["../../../src/data/collector.js"],"names":[],"mappings":"AAUA;;;;;GAKG;AACH;IAkCI;;OAEG;IACH,qBAFW,OAAO,sBAAsB,EAAE,aAAa,EAetD;IAVG,qDAA2C;IAE3C,2CAA2C;IAC3C,WADW,CAAC,CAAS,IAAS,EAAT,SAAS,KAAE,IAAI,CAAC,EAAE,CACpB;IAGnB,yFAAyF;IACzF,cADW,GAAG,CAAC,OAAO,oBAAoB,EAAE,MAAM,EAAE,+BAAO,CACN;IAuHzD;;OAEG;IACH,WAFa,QAAQ,+BAAO,CAqB3B;IAED;;;OAGG;IACH,mBAFW,CAAC,KAAK,+BAAO,KAAK,IAAI,QAUhC;IAED;;OAEG;IACH,uBAMC;IA8CD;;;;OAIG;IACH,8BAFW,MAAM,iCA4BhB;;CACJ;qBA/SyD,eAAe"}

package/dist/src/data/dataFlow.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dataFlow.d.ts","sourceRoot":"","sources":["../../../src/data/dataFlow.js"],"names":[],"mappings":"AAEA;;;GAGG;AACH;IAEQ,gEAAgE;IAChE,oBADW,IAAI,CAAC,EAAE,OAAO,yBAAyB,EAAE,OAAO,CAAC,CACzB;IAEnC,uDAAuD;IACvD,mBADW,IAAI,CAAC,EAAE,OAAO,gBAAgB,EAAE,OAAO,CAAC,CACjB;IAElC,0EAA0E;IAC1E,YADW,IAAI,CAAC,EAAE,QAAU,OAAO,gBAAgB,EAAE,OAAO,KAAE,IAAI,CAAC,EAAE,CAAC,CAC3C;IAG/B,+DAEC;IAED,qDAEC;IAED;;;;;OAKG;IACH,6BAHoB,OAAO,gBAAgB,EAAE,OAAO,KAAE,IAAI,OAC/C,CAAC,QAUX;IAED;;;;OAIG;IACH,kCAHW,OAAO,gBAAgB,EAAE,OAAO,OAChC,CAAC,QAUX;IAED;;;;OAIG;IACH,0BAHW,OAAO,yBAAyB,EAAE,OAAO,OACzC,CAAC,QAIX;IAED;;;OAGG;IACH,yBAFW,CAAC,6CAIX;IAED;;;OAGG;IACH,0BAFW,MAAM;;;MAiChB;IAED;;;;OAIG;IACH,wBAHW,OAAO,gBAAgB,EAAE,OAAO,OAChC,CAAC,QAOX;IAED;;;OAGG;IACH,wBAFW,CAAC,oCAIX;IAED;;;;OAIG;IACH,mBAIC;CACJ;wBA7IuB,0BAA0B"}
+{"version":3,"file":"dataFlow.d.ts","sourceRoot":"","sources":["../../../src/data/dataFlow.js"],"names":[],"mappings":"AAEA;;;GAGG;AACH,8BAHa,CAAC;IAKN,gEAAgE;IAChE,oBADW,GAAG,CAAC,CAAC,EAAE,OAAO,yBAAyB,EAAE,OAAO,CAAC,CACzB;IAEnC,uDAAuD;IACvD,mBADW,GAAG,CAAC,CAAC,EAAE,OAAO,gBAAgB,EAAE,OAAO,CAAC,CACjB;IAElC,0EAA0E;IAC1E,YADW,GAAG,CAAC,CAAC,EAAE,CAAC,CAAS,IAAgC,EAAhC,OAAO,gBAAgB,EAAE,OAAO,KAAE,IAAI,CAAC,EAAE,CAAC,CAC3C;IAG/B,+DAEC;IAED,qDAEC;IAED;;;;;OAKG;IACH,sBAHW,CAAS,IAAgC,EAAhC,OAAO,gBAAgB,EAAE,OAAO,KAAE,IAAI,OAC/C,CAAC,QAUX;IAED;;;;OAIG;IACH,kCAHW,OAAO,gBAAgB,EAAE,OAAO,OAChC,CAAC,QAUX;IAED;;;;OAIG;IACH,0BAHW,OAAO,yBAAyB,EAAE,OAAO,OACzC,CAAC,QAIX;IAED;;;OAGG;IACH,yBAFW,CAAC,6CAIX;IAED;;;OAGG;IACH,0BAFW,MAAM;;;MAiChB;IAED;;;;OAIG;IACH,wBAHW,OAAO,gBAAgB,EAAE,OAAO,OAChC,CAAC,QAOX;IAED;;;OAGG;IACH,wBAFW,CAAC,oCAIX;IAED;;;;OAIG;IACH,mBAIC;CACJ;wBA7IuB,0BAA0B"}

package/dist/src/data/facetNode.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"facetNode.d.ts","sourceRoot":"","sources":["../../../src/data/facetNode.js"],"names":[],"mappings":"AAEA;;;GAGG;AACH;IACI;;OAEG;IACH,oBAFW,WAAW,EAOrB;IAFG,yCAAyC;IACzC,UADW,IAAI,GAAG,GAAG,GAAG,EAAE,EAAE,QAAQ,CAAC,CACZ;CAEhC;;aAZS,MAAM,EAAE;;qBAJG,eAAe"}
+{"version":3,"file":"facetNode.d.ts","sourceRoot":"","sources":["../../../src/data/facetNode.js"],"names":[],"mappings":"AAEA;;;GAGG;AACH;IACI;;OAEG;IACH,oBAFW,WAAW,EAOrB;IAFG,yCAAyC;IACzC,UADW,GAAG,CAAC,GAAG,GAAG,GAAG,EAAE,EAAE,QAAQ,CAAC,CACZ;CAEhC;;aAZS,MAAM,EAAE;;qBAJG,eAAe"}

package/dist/src/data/flowNode.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"flowNode.d.ts","sourceRoot":"","sources":["../../../src/data/flowNode.js"],"names":[],"mappings":"AAuUA;;;GAGG;AACH,uCAHW,OAAO,uBAAuB,EAAE,SAAS,0DAKnD;AAED;;;GAGG;AACH,wCAHW,OAAO,uBAAuB,EAAE,SAAS,2DAKnD;AAnVD;;;GAGG;AACH,qCAAsC;AAEtC;;;GAGG;AACH,uCAAwC;AAExC;;;GAGG;AACH,uCAAwC;AAExC;;GAEG;AAEH;;;;;GAKG;AACH;IA2BI;;OAEG;IACH,oCAFW,qBAAqB,EAa/B;IAxCD;;QAEI,oBAAoB;eAAT,KAAK;MAElB;IAEF;;;;OAIG;IACH,uBAFU,qBAAqB,CAEF;IAE7B,uBAEC;IAED;;;;OAIG;IACH,oBAEC;IAQG,yBAAyB;IACzB,UADW,QAAQ,EAAE,CACH;IAElB,uBAAuB;IACvB,QADW,QAAQ,CACI;IAEvB,2CAA2C;IAC3C,mBAAsB;IAG1B;;;OAGG;IACH,cASC;IAED;;;OAGG;IACH,mBAEC;IAgOD;;;OAGG;IACH,4BAHW,KAAK,QAKf;IA7MD;;;OAGG;IACH,kBAFW,QAAQ,QAIlB;IAED;;;OAGG;IACH,gBAFW,QAAQ,QAUlB;IAED;;OAEG;IACH,YAFW,QAAQ,QAQlB;IAED;;OAEG;IACH,6BAFW,QAAQ,QAMlB;IAED;;OAEG;IACH,0BAFW,QAAQ,QAalB;IAED;;;OAGG;IACH,mBAFW,QAAQ,QAWlB;IAED;;OAEG;IACH,eAiBC;IAED,kBAEC;IAED,uBAEC;IAED,sBAEC;IAED;;;;OAIG;IACH,eAFW,QAAU,QAAQ,KAAE,IAAI,CAAC,GAAG;QAAE,aAAa,CAAC,SAAW,QAAQ,KAAE,IAAI,CAAA;KAAC,QAchF;IAED;;;OAGG;IACH,wBAHW,MAAM,GACJ,MAAM,CAWlB;IAED;;;OAGG;IACH,cAFW,KAAK,QAKf;IAED,iBAMC;IAED;;;;OAIG;IACH,sBAFW,OAAO,uBAAuB,EAAE,SAAS,QAMnD;IAED;;;OAGG;IACH,0EASC;IAED;;;;OAIG;IACH,8BAQC;;CASJ;oCAhTY;IAAC,aAAa,EAAE,OAAO,0BAA0B,EAAE,OAAO,CAAA;CAAC;;;;oBAM3D,OAAO,MAAM,EAAE,GAAG,CAAC;;;;mBACnB,KAAK,EAAE"}
+{"version":3,"file":"flowNode.d.ts","sourceRoot":"","sources":["../../../src/data/flowNode.js"],"names":[],"mappings":"AAuUA;;;GAGG;AACH,uCAHW,OAAO,uBAAuB,EAAE,SAAS,GACvC,SAAS,IAAI,OAAO,uBAAuB,EAAE,SAAS,CAIlE;AAED;;;GAGG;AACH,wCAHW,OAAO,uBAAuB,EAAE,SAAS,GACvC,SAAS,IAAI,OAAO,uBAAuB,EAAE,UAAU,CAInE;AAnVD;;;GAGG;AACH,qCAAsC;AAEtC;;;GAGG;AACH,uCAAwC;AAExC;;;GAGG;AACH,uCAAwC;AAExC;;GAEG;AAEH;;;;;GAKG;AACH;IA2BI;;OAEG;IACH,oCAFW,qBAAqB,EAa/B;IAxCD;;QAEI,oBAAoB;eAAT,KAAK;MAElB;IAEF;;;;OAIG;IACH,uBAFU,qBAAqB,CAEF;IAE7B,uBAEC;IAED;;;;OAIG;IACH,oBAEC;IAQG,yBAAyB;IACzB,UADW,QAAQ,EAAE,CACH;IAElB,uBAAuB;IACvB,QADW,QAAQ,CACI;IAEvB,2CAA2C;IAC3C,mBAAsB;IAG1B;;;OAGG;IACH,cASC;IAED;;;OAGG;IACH,mBAEC;IAgOD;;;OAGG;IACH,4BAHW,KAAK,QAKf;IA7MD;;;OAGG;IACH,kBAFW,QAAQ,QAIlB;IAED;;;OAGG;IACH,gBAFW,QAAQ,QAUlB;IAED;;OAEG;IACH,YAFW,QAAQ,QAQlB;IAED;;OAEG;IACH,6BAFW,QAAQ,QAMlB;IAED;;OAEG;IACH,0BAFW,QAAQ,QAalB;IAED;;;OAGG;IACH,mBAFW,QAAQ,QAWlB;IAED;;OAEG;IACH,eAiBC;IAED,kBAEC;IAED,uBAEC;IAED,sBAEC;IAED;;;;OAIG;IACH,eAFW,CAAC,CAAS,IAAQ,EAAR,QAAQ,KAAE,IAAI,CAAC,GAAG;QAAE,aAAa,CAAC,EAAE,CAAS,IAAQ,EAAR,QAAQ,KAAE,IAAI,CAAA;KAAC,QAchF;IAED;;;OAGG;IACH,wBAHW,MAAM,GACJ,MAAM,CAWlB;IAED;;;OAGG;IACH,cAFW,KAAK,QAKf;IAED,iBAMC;IAED;;;;OAIG;IACH,sBAFW,OAAO,uBAAuB,EAAE,SAAS,QAMnD;IAED;;;OAGG;IACH,0EASC;IAED;;;;OAIG;IACH,8BAQC;;CASJ;oCAhTY;IAAC,aAAa,EAAE,OAAO,0BAA0B,EAAE,OAAO,CAAA;CAAC;;;;oBAM3D,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC;;;;mBACnB,KAAK,EAAE"}

package/dist/src/data/flowNode.js

@@ -252,9 +252,9 @@ export default class FlowNode {
             .map((child) => child.subtreeToString(depth + 1))
             .join("");
         return `${" ".repeat(depth * 2)}* ${this.label}${
-            ("identifier" in this && this.identifier
+            "identifier" in this && this.identifier
                 ? ": " + this.identifier
-                : "") ?? ""
+                : ""
         } \n${childTree}`;
     }
 

package/dist/src/data/sources/dataSourceFactory.d.ts

@@ -2,7 +2,7 @@
  * @param {Partial<import("../../spec/data.js").Data>} params
  * @param {import("../../view/view.js").default} view
  */
-export default function createDataSource(params: Partial<import("../../spec/data.js").Data>, view: import("../../view/view.js").default): InlineSource | UrlSource | SequenceSource | AxisTickSource | AxisGenomeSource | IndexedFastaSource | BigWigSource | BigBedSource | BamSource | Gff3Source;
+export default function createDataSource(params: Partial<import("../../spec/data.js").Data>, view: import("../../view/view.js").default): InlineSource | UrlSource | SequenceSource | AxisTickSource | AxisGenomeSource | IndexedFastaSource | BigWigSource | BigBedSource | BamSource | Gff3Source | VcfSource;
 import InlineSource from "./inlineSource.js";
 import UrlSource from "./urlSource.js";
 import SequenceSource from "./sequenceSource.js";
@@ -13,4 +13,5 @@ import BigWigSource from "./lazy/bigWigSource.js";
 import BigBedSource from "./lazy/bigBedSource.js";
 import BamSource from "./lazy/bamSource.js";
 import Gff3Source from "./lazy/gff3Source.js";
+import VcfSource from "./lazy/vcfSource.js";
 //# sourceMappingURL=dataSourceFactory.d.ts.map

package/dist/src/data/sources/dataSourceFactory.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dataSourceFactory.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/dataSourceFactory.js"],"names":[],"mappings":"AAWA;;;GAGG;AACH,iDAHW,QAAQ,OAAO,oBAAoB,EAAE,IAAI,CAAC,QAC1C,OAAO,oBAAoB,EAAE,OAAO,6JAgB9C;yBA7B0C,mBAAmB;sBACzB,gBAAgB;2BACD,qBAAqB;2BAC9C,0BAA0B;6BACxB,4BAA4B;+BAC1B,8BAA8B;yBACpC,wBAAwB;yBACxB,wBAAwB;sBAC3B,qBAAqB;uBACpB,sBAAsB"}
+{"version":3,"file":"dataSourceFactory.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/dataSourceFactory.js"],"names":[],"mappings":"AAYA;;;GAGG;AACH,iDAHW,OAAO,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,QAC1C,OAAO,oBAAoB,EAAE,OAAO,yKAgB9C;yBA9B0C,mBAAmB;sBACzB,gBAAgB;2BACD,qBAAqB;2BAC9C,0BAA0B;6BACxB,4BAA4B;+BAC1B,8BAA8B;yBACpC,wBAAwB;yBACxB,wBAAwB;sBAC3B,qBAAqB;uBACpB,sBAAsB;sBACvB,qBAAqB"}

package/dist/src/data/sources/dataSourceFactory.js

@@ -8,6 +8,7 @@ import BigWigSource from "./lazy/bigWigSource.js";
 import BigBedSource from "./lazy/bigBedSource.js";
 import BamSource from "./lazy/bamSource.js";
 import Gff3Source from "./lazy/gff3Source.js";
+import VcfSource from "./lazy/vcfSource.js";
 
 /**
  * @param {Partial<import("../../spec/data.js").Data>} params
@@ -100,6 +101,14 @@ function isGff3Source(params) {
     return params?.type == "gff3";
 }
 
+/**
+ * @param {import("../../spec/data.js").LazyDataParams} params
+ * @returns {params is import("../../spec/data.js").VcfData}
+ */
+function isVcfSource(params) {
+    return params?.type == "vcf";
+}
+
 /**
  * @param {import("../../spec/data.js").LazyDataParams} params
  * @param {import("../../view/view.js").default} view
@@ -119,6 +128,8 @@ function createLazyDataSource(params, view) {
         return new BamSource(params, view);
     } else if (isGff3Source(params)) {
         return new Gff3Source(params, view);
+    } else if (isVcfSource(params)) {
+        return new VcfSource(params, view);
     }
 
     throw new Error(

package/dist/src/data/sources/dataUtils.d.ts

@@ -7,15 +7,15 @@
  */
 export function getFormat(params: import("../../spec/data.js").DataSource): {
     type?: "csv" | "tsv";
-    parse?: import("../../spec/data.js").Parse;
+    parse?: import("../../spec/data.js").Parse | null;
 } | {
     type?: "dsv";
     delimiter: string;
-    parse?: import("../../spec/data.js").Parse;
+    parse?: import("../../spec/data.js").Parse | null;
 } | {
     type?: "json";
     property?: string;
-    parse?: import("../../spec/data.js").Parse;
+    parse?: import("../../spec/data.js").Parse | null;
 } | {
     type: string;
 };

package/dist/src/data/sources/dataUtils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dataUtils.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/dataUtils.js"],"names":[],"mappings":"AAIA;;;;;;GAMG;AACH,kCAHW,OAAO,oBAAoB,EAAE,UAAU;;;;;;;;;;;;;EAsBjD;AAED;;;GAGG;AACH,mCAHW,MAAM,GACJ,MAAM,CAIlB;AAED;;GAEG;AACH,wCAFW,MAAM,GAAG,MAAM,EAAE,UAU3B;AAWD;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,UAAU,4DAKjD;AAED;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,UAAU,4DAKjD;AAED;;;GAGG;AACH,6CAHW,OAAO,oBAAoB,EAAE,UAAU,6DAKjD;AAED;;;;GAIG;AACH,sCAHW,OAAO,oBAAoB,EAAE,UAAU,sDAKjD;AAxCM,+BAAgC,GAAG,QAI3B,OAAO,uBAAuB,EAAE,MAAM;;UAGtB,OAAO,gBAAgB,EAAE,KAAK,qCANR"}
+{"version":3,"file":"dataUtils.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/dataUtils.js"],"names":[],"mappings":"AAIA;;;;;;GAMG;AACH,kCAHW,OAAO,oBAAoB,EAAE,UAAU;;;;;;;;;;;;;EAsBjD;AAED;;;GAGG;AACH,mCAHW,MAAM,GACJ,MAAM,CAIlB;AAED;;GAEG;AACH,wCAFW,MAAM,GAAG,MAAM,EAAE,UAU3B;AAWD;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,UAAU,GACtC,UAAU,IAAI,OAAO,oBAAoB,EAAE,aAAa,CAInE;AAED;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,UAAU,GACtC,UAAU,IAAI,OAAO,oBAAoB,EAAE,aAAa,CAInE;AAED;;;GAGG;AACH,6CAHW,OAAO,oBAAoB,EAAE,UAAU,GACtC,UAAU,IAAI,OAAO,oBAAoB,EAAE,cAAc,CAIpE;AAED;;;;GAIG;AACH,sCAHW,OAAO,oBAAoB,EAAE,UAAU,GACtC,UAAU,IAAI,OAAO,oBAAoB,EAAE,OAAO,CAI7D;AAxCM,+BAAgC,GAAG,QAI3B,OAAO,uBAAuB,EAAE,MAAM;;UAGtB,OAAO,gBAAgB,EAAE,KAAK,qCANR"}

package/dist/src/data/sources/inlineSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"inlineSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/inlineSource.js"],"names":[],"mappings":"AAIA;;;GAGG;AACH,mCAHW,QAAQ,OAAO,oBAAoB,EAAE,IAAI,CAAC,mDAKpD;AAED;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,UAAU,QACvC,OAAO,oBAAoB,EAAE,OAAO,EAY9C;IAPG,gDAAoB;IAaxB;;OAEG;IACH,qBASC;IAED,0BAiCC;CAKJ;uBAnFsB,iBAAiB"}
+{"version":3,"file":"inlineSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/inlineSource.js"],"names":[],"mappings":"AAIA;;;GAGG;AACH,mCAHW,OAAO,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,GACxC,IAAI,IAAI,OAAO,oBAAoB,EAAE,UAAU,CAI3D;AAED;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,UAAU,QACvC,OAAO,oBAAoB,EAAE,OAAO,EAY9C;IAPG,gDAAoB;IAaxB;;OAEG;IACH,qBASC;IAED,0BAiCC;CAKJ;uBAnFsB,iBAAiB"}

package/dist/src/data/sources/lazy/bamSource.js

@@ -92,13 +92,13 @@ export default class BamSource extends SingleAxisWindowedSource {
                     .then((records) =>
                         records.map((record) => ({
                             chrom: d.chrom,
-                            start: record.get("start"),
-                            end: record.get("end"),
-                            name: record.get("name"),
-                            MD: record.get("MD"),
-                            cigar: record.get("cigar"),
-                            mapq: record.get("mq"),
-                            strand: record.get("strand") === 1 ? "+" : "-",
+                            start: record.start,
+                            end: record.end,
+                            name: record.name,
+                            //MD: record.get("MD"),
+                            cigar: record.CIGAR,
+                            mapq: record.mq,
+                            strand: record.strand === 1 ? "+" : "-",
                         }))
                     )
         );

package/dist/src/data/sources/lazy/bigBedSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"bigBedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bigBedSource.js"],"names":[],"mappings":"AAOA;IAUI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,UAAU,QAC1C,OAAO,uBAAuB,EAAE,OAAO,EAmCjD;IA9CD,0CAA0C;IAC1C,QADW,OAAO,WAAW,EAAE,OAAO,CAC/B;IAEP,yCAAyC;IACzC,KADW,OAAO,WAAW,EAAE,MAAM,CACjC;IAEJ,4GAA4G;IAC5G,WADW,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAC;QAAC,IAAI,CAAC,EAAE,MAAM,CAAA;KAAE,KAAK,OAAO,MAAM,EAAE,GAAG,CAAC,CAC9F;IA8BN,mDAA6B;;CAwFpC;qCAhIoC,+BAA+B"}
+{"version":3,"file":"bigBedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bigBedSource.js"],"names":[],"mappings":"AAOA;IAUI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,UAAU,QAC1C,OAAO,uBAAuB,EAAE,OAAO,EAmCjD;IA9CD,0CAA0C;IAC1C,QADW,OAAO,WAAW,EAAE,OAAO,CAC/B;IAEP,yCAAyC;IACzC,KADW,OAAO,WAAW,EAAE,MAAM,CACjC;IAEJ,4GAA4G;IAC5G,WADW,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAC;QAAC,IAAI,CAAC,EAAE,MAAM,CAAA;KAAE,KAAK,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAC9F;IA8BN,mDAA6B;;CAwFpC;qCAhIoC,+BAA+B"}

package/dist/src/data/sources/lazy/gff3Source.d.ts

@@ -2,11 +2,9 @@
  * @extends {TabixSource<import("@gmod/gff").GFF3Feature>}
  */
 export default class Gff3Source extends TabixSource<import("@gmod/gff").GFF3Feature> {
-    /**
-     * @param {import("../../../spec/data.js").TabixData} params
-     * @param {import("../../../view/view.js").default} view
-     */
-    constructor(params: import("../../../spec/data.js").TabixData, view: import("../../../view/view.js").default);
+    constructor(params: import("../../../spec/data.js").TabixData, view: import("../../../view/view.js" /**
+     * @param {string[]} lines
+     */).default);
     /**
      * @param {string[]} lines
      */

package/dist/src/data/sources/lazy/gff3Source.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"gff3Source.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/gff3Source.js"],"names":[],"mappings":"AAEA;;GAEG;AACH;IAII;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,SAAS,QACzC,OAAO,uBAAuB,EAAE,OAAO,EASjD;IAMD;;OAEG;IACH,sBAFW,MAAM,EAAE,OAUlB;;CACJ;wBAtCuB,kBAAkB"}
+{"version":3,"file":"gff3Source.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/gff3Source.js"],"names":[],"mappings":"AAEA;;GAEG;AACH;+BAWU,uBAAuB,0BACQ,uBAGzC,CAAI;;OAEG;IAFH;;OAEG;IACH,sBAFW,MAAM,EAAE,OAUlB;;CACJ;wBAhCuB,kBAAkB"}

package/dist/src/data/sources/lazy/gff3Source.js

@@ -7,23 +7,17 @@ export default class Gff3Source extends TabixSource {
     /** @type {import("@gmod/gff").default} */
     #gff;
 
-    /**
-     * @param {import("../../../spec/data.js").TabixData} params
-     * @param {import("../../../view/view.js").default} view
-     */
-    constructor(params, view) {
-        super(params, view);
-
-        import("@gmod/gff").then((gff) => {
-            // TODO: Fix race condition
-            this.#gff = gff.default;
-        });
-    }
-
     get label() {
         return "gff3Source";
     }
 
+    /**
+     * @param {string} header
+     */
+    async _handleHeader(header) {
+        this.#gff = (await import("@gmod/gff")).default;
+    }
+
     /**
      * @param {string[]} lines
      */

package/dist/src/data/sources/lazy/singleAxisWindowedSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"singleAxisWindowedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisWindowedSource.js"],"names":[],"mappings":"AAIA;;;;;GAKG;AACH;IAWI;;;OAGG;IACH,kBAHU;QAAC,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,4BAA4B,EAAE,OAAO,CAAA;KAAC,CAGvE;IAEP;;;OAGG;IACH,0CAHW,OAAO,uBAAuB,EAAE,aAAa,QAqBvD;IAED;;;;OAIG;IACH,wBAFW,MAAM,EAAE,QAqBlB;IAcD;;;;;OAKG;IACH,iCAHW,MAAM,EAAE,iBAKlB;IApBD;;OAEG;IACH,mCAOC;IAYD;;;;;;;;;OASG;IACH,yCANW,MAAM,EAAE,4BACU,OAAO,mCAAmC,EAAE,0BAA0B,UAAU,WAAW,+BAqCvH;IAED;;;;;;OAMG;IACH,yCALW,MAAM,EAAE,cACR,MAAM,mBACG,MAAM,EAAE,KAAE,IAAI,QAyBjC;;CACJ;iCA3KgC,2BAA2B"}
+{"version":3,"file":"singleAxisWindowedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisWindowedSource.js"],"names":[],"mappings":"AAIA;;;;;GAKG;AACH;IAWI;;;OAGG;IACH,kBAHU;QAAC,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,4BAA4B,EAAE,OAAO,CAAA;KAAC,CAGvE;IAEP;;;OAGG;IACH,0CAHW,OAAO,uBAAuB,EAAE,aAAa,QAqBvD;IAED;;;;OAIG;IACH,wBAFW,MAAM,EAAE,QAqBlB;IAcD;;;;;OAKG;IACH,iCAHW,MAAM,EAAE,iBAKlB;IApBD;;OAEG;IACH,mCAOC;IAYD;;;;;;;;;OASG;IACH,4BAHa,CAAC,YAHH,MAAM,EAAE,UACR,CAAC,eAAe,EAAE,OAAO,mCAAmC,EAAE,0BAA0B,EAAE,MAAM,EAAE,WAAW,KAAK,OAAO,CAAC,CAAC,CAAC,GAC3H,OAAO,CAAC,CAAC,EAAE,CAAC,CAoCvB;IAED;;;;;;OAMG;IACH,yCALW,MAAM,EAAE,cACR,MAAM,YACN,CAAS,IAAQ,EAAR,MAAM,EAAE,KAAE,IAAI,QAyBjC;;CACJ;iCA3KgC,2BAA2B"}

package/dist/src/data/sources/lazy/tabixSource.d.ts

@@ -10,6 +10,11 @@ export default class TabixSource<T> extends SingleAxisWindowedSource {
     constructor(params: import("../../../spec/data.js").TabixData, view: import("../../../view/view.js").default);
     params: import("../../../spec/data.js").TabixData;
     initializedPromise: Promise<any>;
+    /**
+     * @param {string} header
+     * @protected
+     */
+    protected _handleHeader(header: string): Promise<void>;
     /**
      * @abstract
      * @protected

package/dist/src/data/sources/lazy/tabixSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"tabixSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/tabixSource.js"],"names":[],"mappings":"AAGA;;;GAGG;AACH;IAII;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,SAAS,QACzC,OAAO,uBAAuB,EAAE,OAAO,EA8CjD;IAhCG,kDAAgC;IAQhC,iCAuBE;IAoCN;;;;;OAKG;IACH,gCAHW,MAAM,EAAE,GACN,CAAC,EAAE,CAKf;;CACJ;qCAvGoC,+BAA+B"}
+{"version":3,"file":"tabixSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/tabixSource.js"],"names":[],"mappings":"AAGA;;;GAGG;AACH,iCAHa,CAAC;IAOV;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,SAAS,QACzC,OAAO,uBAAuB,EAAE,OAAO,EAkDjD;IAnCG,kDAAgC;IAQhC,iCA0BE;IAqCN;;;OAGG;IACH,gCAHW,MAAM,iBAKhB;IAED;;;;;OAKG;IACH,gCAHW,MAAM,EAAE,GACN,CAAC,EAAE,CAKf;;CACJ;qCApHoC,+BAA+B"}

package/dist/src/data/sources/lazy/tabixSource.js

@@ -20,6 +20,7 @@ export default class TabixSource extends SingleAxisWindowedSource {
             windowSize: 3_000_000,
             debounce: 200,
             debounceMode: "domain",
+            addChrPrefix: false,
             ...params,
         };
 
@@ -35,15 +36,9 @@ export default class TabixSource extends SingleAxisWindowedSource {
 
         this.initializedPromise = new Promise((resolve) => {
             Promise.all([
-                import("buffer"),
                 import("@gmod/tabix"),
                 import("generic-filehandle"),
-            ]).then(([{ Buffer }, { TabixIndexedFile }, { RemoteFile }]) => {
-                // Hack needed by @gmod/tabix
-                if (typeof window !== "undefined") {
-                    window.Buffer ??= Buffer;
-                }
-
+            ]).then(async ([{ TabixIndexedFile }, { RemoteFile }]) => {
                 const withBase = (/** @type {string} */ uri) =>
                     new RemoteFile(addBaseUrl(uri, this.view.getBaseUrl()));
 
@@ -52,8 +47,17 @@ export default class TabixSource extends SingleAxisWindowedSource {
                     tbiFilehandle: withBase(
                         this.params.indexUrl ?? this.params.url + ".tbi"
                     ),
+                    renameRefSeqs:
+                        this.params.addChrPrefix === true
+                            ? (refSeq) => "chr" + refSeq
+                            : this.params.addChrPrefix
+                              ? (refSeq) => this.params.addChrPrefix + refSeq
+                              : undefined,
                 });
 
+                const header = await this.#tbiIndex.getHeader();
+                await this._handleHeader(header);
+
                 resolve();
             });
         });
@@ -65,6 +69,7 @@ export default class TabixSource extends SingleAxisWindowedSource {
      * @param {number[]} interval linearized domain
      */
     async loadInterval(interval) {
+        await this.initializedPromise;
         const featureChunks = await this.discretizeAndLoad(
             interval,
             async (discreteInterval, signal) => {
@@ -92,6 +97,14 @@ export default class TabixSource extends SingleAxisWindowedSource {
         }
     }
 
+    /**
+     * @param {string} header
+     * @protected
+     */
+    async _handleHeader(header) {
+        //
+    }
+
     /**
      * @abstract
      * @protected

package/dist/src/data/sources/lazy/vcfSource.d.ts

@@ -0,0 +1,9 @@
+/**
+ * @extends {TabixSource<import("./vcfTypes.js").ParsedVariant>}
+ */
+export default class VcfSource extends TabixSource<import("./vcfTypes.js").ParsedVariant> {
+    constructor(params: import("../../../spec/data.js").TabixData, view: import("../../../view/view.js").default);
+    #private;
+}
+import TabixSource from "./tabixSource.js";
+//# sourceMappingURL=vcfSource.d.ts.map

package/dist/src/data/sources/lazy/vcfSource.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"vcfSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/vcfSource.js"],"names":[],"mappings":"AAEA;;GAEG;AACH;+BAUK,uBACe,0BACQ,uBAAuB;;CAoBlD;wBArCuB,kBAAkB"}

package/dist/src/data/sources/lazy/vcfSource.js

@@ -0,0 +1,38 @@
+import TabixSource from "./tabixSource.js";
+
+/**
+ * @extends {TabixSource<import("./vcfTypes.js").ParsedVariant>}
+ */
+export default class VcfSource extends TabixSource {
+    /** @type {import("@gmod/vcf").default} */
+    #tbiVCFParser;
+
+    get label() {
+        return "vcfSource";
+    }
+
+    /**
+     * @param {string} header
+     */
+    async _handleHeader(header) {
+        const VCFParser = (await import("@gmod/vcf")).default;
+        // @ts-ignore - There's something wrong with the type definition
+        this.#tbiVCFParser = new VCFParser({ header });
+    }
+
+    /**
+     * @param {string[]} lines
+     */
+    _parseFeatures(lines) {
+        return lines.map((line) => {
+            const parsed = this.#tbiVCFParser.parseLine(line);
+            delete parsed.GENOTYPES;
+            // @ts-ignore
+            parsed.SAMPLES = parsed.SAMPLES();
+
+            return /** @type {import("./vcfTypes.js").ParsedVariant} */ (
+                /** @type {object} */ (parsed)
+            );
+        });
+    }
+}

package/dist/src/data/sources/lazy/vcfTypes.d.ts

@@ -0,0 +1,7 @@
+import { Variant } from "@gmod/vcf";
+
+type Samples = ReturnType<Variant["SAMPLES"]>;
+
+export type ParsedVariant = Omit<Variant, "SAMPLES" | "GENOTYPES"> & {
+    SAMPLES: Samples;
+};

package/dist/src/data/sources/namedSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"namedSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/namedSource.js"],"names":[],"mappings":"AAGA;;;GAGG;AACH,kCAHW,QAAQ,OAAO,oBAAoB,EAAE,IAAI,CAAC,kDAKpD;AAED;IAOI;;;;OAIG;IACH,oBAJW,OAAO,oBAAoB,EAAE,SAAS,QACtC,OAAO,oBAAoB,EAAE,OAAO,mBAC3B,MAAM,KAAE,GAAG,EAAE,EAOhC;IAFG,iBALgB,MAAM,KAAE,GAAG,EAAE,CAKL;IACxB,+CAAoB;IAcxB;;;;OAIG;IACH,yBAFW,OAAO,gBAAgB,EAAE,KAAK,EAAE,QAM1C;IAED,0BA0BC;;CAKJ;uBAnFsB,iBAAiB"}
+{"version":3,"file":"namedSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/namedSource.js"],"names":[],"mappings":"AAGA;;;GAGG;AACH,kCAHW,OAAO,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,GACxC,IAAI,IAAI,OAAO,oBAAoB,EAAE,SAAS,CAI1D;AAED;IAOI;;;;OAIG;IACH,oBAJW,OAAO,oBAAoB,EAAE,SAAS,QACtC,OAAO,oBAAoB,EAAE,OAAO,YACpC,CAAS,IAAM,EAAN,MAAM,KAAE,GAAG,EAAE,EAOhC;IAFG,iBALgB,MAAM,KAAE,GAAG,EAAE,CAKL;IACxB,+CAAoB;IAcxB;;;;OAIG;IACH,yBAFW,OAAO,gBAAgB,EAAE,KAAK,EAAE,QAM1C;IAED,0BA0BC;;CAKJ;uBAnFsB,iBAAiB"}

package/dist/src/data/sources/sequenceSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sequenceSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/sequenceSource.js"],"names":[],"mappings":"AAMA;;;GAGG;AACH,0CAHW,QAAQ,OAAO,oBAAoB,EAAE,IAAI,CAAC,0DAKpD;AAED;IACI;;;;OAIG;IACH,oBAHW,OAAO,oBAAoB,EAAE,iBAAiB,QAC9C,OAAO,oBAAoB,EAAE,OAAO,EAiB9C;IAZG,sDAIC;IAcL,0BAcC;CAKJ;uBAxDsB,iBAAiB"}
+{"version":3,"file":"sequenceSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/sequenceSource.js"],"names":[],"mappings":"AAMA;;;GAGG;AACH,0CAHW,OAAO,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,GACxC,IAAI,IAAI,OAAO,oBAAoB,EAAE,iBAAiB,CAIlE;AAED;IACI;;;;OAIG;IACH,oBAHW,OAAO,oBAAoB,EAAE,iBAAiB,QAC9C,OAAO,oBAAoB,EAAE,OAAO,EAiB9C;IAZG,sDAIC;IAcL,0BAcC;CAKJ;uBAxDsB,iBAAiB"}

package/dist/src/data/sources/urlSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"urlSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/urlSource.js"],"names":[],"mappings":"AASA;;;GAGG;AACH,gCAHW,QAAQ,OAAO,oBAAoB,EAAE,IAAI,CAAC,gDAKpD;AAED;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAU9C;IALG,6CAEC;IAED,gBAAiC;CA0ExC;uBArGsB,iBAAiB"}
+{"version":3,"file":"urlSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/urlSource.js"],"names":[],"mappings":"AASA;;;GAGG;AACH,gCAHW,OAAO,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,GACxC,IAAI,IAAI,OAAO,oBAAoB,EAAE,OAAO,CAIxD;AAED;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAU9C;IALG,6CAEC;IAED,gBAAiC;CA0ExC;uBArGsB,iBAAiB"}

package/dist/src/data/transforms/aggregate.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"aggregate.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregate.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAJW,OAAO,yBAAyB,EAAE,eAAe,EA6C3D;IAvCG,0DAAoB;IAEpB,oBAAoB;IACpB,QADW,GAAG,EAAE,CACA;IAEhB;;OAEG;IACH,iDAF6B,MAAM,IAEtB;IACb;;OAEG;IACH,IAFU,MAAM,EAAE,CAEN;CAiFnB;sBA5GqB,gBAAgB"}
+{"version":3,"file":"aggregate.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregate.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAJW,OAAO,yBAAyB,EAAE,eAAe,EA6C3D;IAvCG,0DAAoB;IAEpB,oBAAoB;IACpB,QADW,GAAG,EAAE,CACA;IAEhB;;OAEG;IACH,KAFU,CAAC,CAAC,GAAG,EAAE,gCAAO,KAAK,MAAM,CAAC,EAAE,CAEzB;IACb;;OAEG;IACH,IAFU,MAAM,EAAE,CAEN;CAiFnB;sBA5GqB,gBAAgB"}

package/dist/src/data/transforms/aggregateOps.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"aggregateOps.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregateOps.js"],"names":[],"mappings":";AAEA;;GAEG;AACH,6BAFU,OAAO,OAAO,yBAAyB,EAAE,WAAW,EAAE,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,GAAG,KAAK,MAAM,KAAK,MAAM,CAAC,CAWxH"}
+{"version":3,"file":"aggregateOps.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregateOps.js"],"names":[],"mappings":";AAEA;;GAEG;AACH,6BAFU,MAAM,CAAC,OAAO,yBAAyB,EAAE,WAAW,EAAE,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,GAAG,KAAK,MAAM,KAAK,MAAM,CAAC,CAWxH"}

package/dist/src/data/transforms/coverage.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="external-typings/flatqueue.js" />
 /**
  * Computes coverage for sorted segments
  *

package/dist/src/data/transforms/coverage.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"coverage.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/coverage.js"],"names":[],"mappings":";AAMA;;;;;;;GAOG;AACH;IAKI;;OAEG;IAEH;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,cAAc,EAgD1D;IA5CG,yDAAoB;IAEpB,mDAAwC;IACxC,iDAAoC;IAEpC,mCAAmC;IACnC,sBADoB,GAAG,KAAE,MAAM,CAGT;IACtB,mCAAmC;IACnC,uBADoB,GAAG,KAAE,MAAM,CACsC;IAErE;;;;;MAKC;IAED,sEACsE,MAAM,oCAgBvE;IAEL;;;;OAIG;IACH,MAFU,UAAU,MAAM,CAAC,CAEA;CA0IlC;sBA7MqB,gBAAgB;sBAJhB,WAAW"}
+{"version":3,"file":"coverage.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/coverage.js"],"names":[],"mappings":"AAMA;;;;;;;GAOG;AACH;IAKI;;OAEG;IAEH;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,cAAc,EAgD1D;IA5CG,yDAAoB;IAEpB,mDAAwC;IACxC,iDAAoC;IAEpC,mCAAmC;IACnC,eADW,CAAS,IAAG,EAAH,GAAG,KAAE,MAAM,CAGT;IACtB,mCAAmC;IACnC,gBADW,CAAS,IAAG,EAAH,GAAG,KAAE,MAAM,CACsC;IAErE;;;;;MAKC;IAED,sEACsE,MAAM,oCAgBvE;IAEL;;;;OAIG;IACH,MAFU,SAAS,CAAC,MAAM,CAAC,CAEA;CA0IlC;sBA7MqB,gBAAgB;sBAJhB,WAAW"}

package/dist/src/data/transforms/filter.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"filter.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filter.js"],"names":[],"mappings":"AA8CA;;;GAGG;AACH,2CAHW,OAAO,yBAAyB,EAAE,YAAY,gEAKxD;AAED;;;GAGG;AACH,gDAHW,OAAO,yBAAyB,EAAE,YAAY,qEAKxD;AAzDD;IACI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,YAAY,yBAC9C,OAAO,gBAAgB,EAAE,qBAAqB,EASxD;IAJG,uDAAoB;IAEpB,oEAAoE;IACpE,WADW,OAAO,6BAA6B,EAAE,eAAe,CACtC;CA6BjC;sBA3CqB,gBAAgB"}
+{"version":3,"file":"filter.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filter.js"],"names":[],"mappings":"AA8CA;;;GAGG;AACH,2CAHW,OAAO,yBAAyB,EAAE,YAAY,GAC5C,MAAM,IAAI,OAAO,yBAAyB,EAAE,gBAAgB,CAIxE;AAED;;;GAGG;AACH,gDAHW,OAAO,yBAAyB,EAAE,YAAY,GAC5C,MAAM,IAAI,OAAO,yBAAyB,EAAE,qBAAqB,CAI7E;AAzDD;IACI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,YAAY,yBAC9C,OAAO,gBAAgB,EAAE,qBAAqB,EASxD;IAJG,uDAAoB;IAEpB,oEAAoE;IACpE,WADW,OAAO,6BAA6B,EAAE,eAAe,CACtC;CA6BjC;sBA3CqB,gBAAgB"}

package/dist/src/data/transforms/filterScoredLabels.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EA2C9C;IAtCG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,iDAAyC;IACzC,mDAA6C;IAC7C,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,qBADoB,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,IAAI,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,4DAAuD;IAIvD,qBAAuE;IAgBvE,eAAiD;IAWrD,4BAyCC;IAKG,sBAAuB;CAU9B;sBA9HqB,gBAAgB;2BAFX,+BAA+B"}
+{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EA2C9C;IAtCG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,iDAAyC;IACzC,mDAA6C;IAC7C,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,cADW,CAAS,IAAG,EAAH,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,GAAG,CAAC,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,4DAAuD;IAIvD,qBAAuE;IAgBvE,eAAiD;IAWrD,4BAyCC;IAKG,sBAAuB;CAU9B;sBA9HqB,gBAAgB;2BAFX,+BAA+B"}

package/dist/src/data/transforms/linearizeGenomicCoordinate.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"linearizeGenomicCoordinate.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/linearizeGenomicCoordinate.js"],"names":[],"mappings":"AAKA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,gCAAgC,QAClE,OAAO,oBAAoB,EAAE,OAAO,EAyF9C;IAhFG,2EAAoB;CAiF3B;sBApGqB,gBAAgB"}
+{"version":3,"file":"linearizeGenomicCoordinate.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/linearizeGenomicCoordinate.js"],"names":[],"mappings":"AAKA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,gCAAgC,QAClE,OAAO,oBAAoB,EAAE,OAAO,EAgG9C;IAvFG,2EAAoB;CAwF3B;sBA3GqB,gBAAgB"}

package/dist/src/data/transforms/linearizeGenomicCoordinate.js

@@ -87,7 +87,7 @@ export default class LinearizeGenomicCoordinate extends Transform {
             if (chrom !== lastChrom) {
                 chromOffset = genome.cumulativeChromPositions.get(chrom);
                 if (chromOffset === undefined) {
-                    throw new Error("Unknown chromosome/contig: " + chrom);
+                    return;
                 }
                 lastChrom = chrom;
             }
@@ -97,7 +97,14 @@ export default class LinearizeGenomicCoordinate extends Transform {
 
         /** @param {Record<string, any>} datum */
         this.handle = (datum) => {
-            setter(datum, getChromOffset(chromAccessor(datum)), posAccessors);
+            const chrom = chromAccessor(datum);
+            const chromOffset = getChromOffset(chrom);
+            if (chromOffset === undefined) {
+                throw new Error(
+                    `Unknown chromosome/contig "${chrom}" in datum: ${JSON.stringify(datum)}`
+                );
+            }
+            setter(datum, chromOffset, posAccessors);
             this._propagate(datum);
         };
     }