@gmod/tabix 1.5.11 → 1.5.13

package/dist/util.js

@@ -74,12 +74,7 @@ function optimizeChunks(chunks, lowest) {
     }
     chunks.sort(function (c0, c1) {
         const dif = c0.minv.blockPosition - c1.minv.blockPosition;
-        if (dif !== 0) {
-            return dif;
-        }
-        else {
-            return c0.minv.dataPosition - c1.minv.dataPosition;
-        }
+        return dif !== 0 ? dif : c0.minv.dataPosition - c1.minv.dataPosition;
     });
     chunks.forEach(chunk => {
         if (!lowest || chunk.maxv.compareTo(lowest) > 0) {

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;AAGA,SAAgB,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AARD,oCAQC;AAED,MAAM,UAAW,SAAQ,KAAK;CAE7B;AACD;;;;;;;;;;GAUG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,qCAAqC;YACrC,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;IACH,CAAC;AACH,CAAC;AAfD,4CAeC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;QACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;QACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAC1B,CAAC;CAAA;AAHD,0CAGC;AAED,SAAgB,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AALD,wCAKC;AAED,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAqB;IACnE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAAS,GAAiB,IAAI,CAAA;IAElC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;IAED,MAAM,CAAC,IAAI,CAAC,UAAU,EAAE,EAAE,EAAE;QAC1B,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;QACrB,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;YAChD,IAAI,SAAS,KAAK,IAAI,EAAE,CAAC;gBACvB,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE,CAAC;oBACrC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC7C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;oBAC7B,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC,CAAC,CAAA;IAEF,OAAO,YAAY,CAAA;AACrB,CAAC;AAhCD,wCAgCC"}

package/dist/virtualOffset.js.map

@@ -1 +1 @@
-{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AACA,MAAqB,aAAa;IAGhC,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE;YACnB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;SACd;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC9B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE;gBAC9B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;aACd;SACF;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AA/BD,gCA+BC;AACD,SAAgB,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;KACnE;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC;AAdD,8BAcC"}
+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AACA,MAAqB,aAAa;IAGhC,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACpB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AA/BD,gCA+BC;AACD,SAAgB,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC;AAdD,8BAcC"}

package/esm/chunk.d.ts

@@ -4,12 +4,6 @@ export default class Chunk {
     maxv: VirtualOffset;
     bin: number;
     _fetchedSize?: number;
-    /**
-     * @param {VirtualOffset} minv
-     * @param {VirtualOffset} maxv
-     * @param {number} bin
-     * @param {number} [fetchedSize]
-     */
     constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?: undefined);
     toUniqueString(): string;
     toString(): string;

package/esm/chunk.js

@@ -1,11 +1,5 @@
 // little class representing a chunk in the index
 export default class Chunk {
-    /**
-     * @param {VirtualOffset} minv
-     * @param {VirtualOffset} maxv
-     * @param {number} bin
-     * @param {number} [fetchedSize]
-     */
     constructor(minv, maxv, bin, fetchedSize = undefined) {
         this.minv = minv;
         this.maxv = maxv;
@@ -13,6 +7,7 @@ export default class Chunk {
         this._fetchedSize = fetchedSize;
     }
     toUniqueString() {
+        // eslint-disable-next-line @typescript-eslint/restrict-template-expressions
         return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
     }
     toString() {

package/esm/chunk.js.map

@@ -1 +1 @@
-{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAMxB;;;;;OAKG;IACH,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,SAAS;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE;YACnC,OAAO,IAAI,CAAC,YAAY,CAAA;SACzB;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}
+{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,SAAS;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,4EAA4E;QAC5E,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}

package/esm/csi.d.ts

@@ -9,12 +9,10 @@ export default class CSI extends IndexFile {
     private minShift;
     constructor(args: any);
     lineCount(refName: string, opts?: Options): Promise<number>;
-    indexCov(): Promise<void>;
+    indexCov(): void;
     parseAuxData(bytes: Buffer, offset: number): {
         refIdToName: string[];
-        refNameToId: {
-            [key: string]: number;
-        };
+        refNameToId: Record<string, number>;
         skipLines: number;
         metaChar: string | null;
         columnNumbers: {
@@ -26,9 +24,7 @@ export default class CSI extends IndexFile {
         coordinateType: string;
     };
     _parseNameBytes(namesBytes: Buffer): {
-        refNameToId: {
-            [key: string]: number;
-        };
+        refNameToId: Record<string, number>;
         refIdToName: string[];
     };
     _parse(opts?: Options): Promise<{
@@ -38,9 +34,7 @@ export default class CSI extends IndexFile {
         firstDataLine: VirtualOffset | undefined;
         csiVersion: number;
         indices: {
-            binIndex: {
-                [key: string]: Chunk[];
-            };
+            binIndex: Record<string, Chunk[]>;
             stats: {
                 lineCount: number;
             } | undefined;
@@ -49,9 +43,7 @@ export default class CSI extends IndexFile {
         maxBinNumber: number;
         maxRefLength: number;
         refIdToName: string[];
-        refNameToId: {
-            [key: string]: number;
-        };
+        refNameToId: Record<string, number>;
         skipLines: number;
         metaChar: string | null;
         columnNumbers: {
@@ -68,9 +60,7 @@ export default class CSI extends IndexFile {
         firstDataLine: VirtualOffset | undefined;
         csiVersion: number;
         indices: {
-            binIndex: {
-                [key: string]: Chunk[];
-            };
+            binIndex: Record<string, Chunk[]>;
             stats: {
                 lineCount: number;
             } | undefined;

package/esm/csi.js

@@ -35,7 +35,7 @@ export default class CSI extends IndexFile {
         }
         return -1;
     }
-    async indexCov() {
+    indexCov() {
         throw new Error('CSI indexes do not support indexcov');
     }
     parseAuxData(bytes, offset) {
@@ -86,7 +86,7 @@ export default class CSI extends IndexFile {
     }
     // fetch and parse the index
     async _parse(opts = {}) {
-        const bytes = await unzip((await this.filehandle.readFile(opts)));
+        const bytes = await unzip(await this.filehandle.readFile(opts));
         // check TBI magic numbers
         let csiVersion;
         if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
@@ -187,9 +187,8 @@ export default class CSI extends IndexFile {
         for (const [start, end] of overlappingBins) {
             for (let bin = start; bin <= end; bin++) {
                 if (ba.binIndex[bin]) {
-                    const binChunks = ba.binIndex[bin];
-                    for (let c = 0; c < binChunks.length; ++c) {
-                        chunks.push(new Chunk(binChunks[c].minv, binChunks[c].maxv, bin));
+                    for (const c of ba.binIndex[bin]) {
+                        chunks.push(new Chunk(c.minv, c.maxv, bin));
                     }
                 }
             }

package/esm/csi.js.map

@@ -1 +1 @@
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package/esm/index.d.ts

@@ -1,4 +1,3 @@
-import TabixIndexedFile from './tabixIndexedFile';
-import TBI from './tbi';
-import CSI from './csi';
-export { TabixIndexedFile, TBI, CSI };
+export { default as TabixIndexedFile } from './tabixIndexedFile';
+export { default as CSI } from './csi';
+export { default as TBI } from './tbi';

package/esm/index.js

@@ -1,5 +1,4 @@
-import TabixIndexedFile from './tabixIndexedFile';
-import TBI from './tbi';
-import CSI from './csi';
-export { TabixIndexedFile, TBI, CSI };
+export { default as TabixIndexedFile } from './tabixIndexedFile';
+export { default as CSI } from './csi';
+export { default as TBI } from './tbi';
 //# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,GAAG,MAAM,OAAO,CAAA;AAEvB,OAAO,EAAE,gBAAgB,EAAE,GAAG,EAAE,GAAG,EAAE,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AAChE,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,OAAO,CAAA;AACtC,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,OAAO,CAAA"}

package/esm/indexFile.d.ts

@@ -6,9 +6,7 @@ export interface Options {
     signal?: AbortSignal;
 }
 export interface IndexData {
-    refNameToId: {
-        [key: string]: number;
-    };
+    refNameToId: Record<string, number>;
     refIdToName: string[];
     metaChar: string | null;
     columnNumbers: {
@@ -32,9 +30,7 @@ export default abstract class IndexFile {
     protected abstract _parse(opts: Options): Promise<IndexData>;
     getMetadata(opts?: Options): Promise<{
         [key: string]: any;
-        refNameToId: {
-            [key: string]: number;
-        };
+        refNameToId: Record<string, number>;
         refIdToName: string[];
         metaChar: string | null;
         columnNumbers: {

package/esm/indexFile.js

@@ -4,8 +4,7 @@ export default class IndexFile {
         this.renameRefSeq = renameRefSeqs;
     }
     async getMetadata(opts = {}) {
-        // eslint-disable-next-line @typescript-eslint/no-unused-vars
-        const { indices, ...rest } = await this.parse(opts);
+        const { indices: _indices, ...rest } = await this.parse(opts);
         return rest;
     }
     _findFirstData(currentFdl, virtualOffset) {
@@ -28,7 +27,9 @@ export default class IndexFile {
         return this.parseP;
     }
     async hasRefSeq(seqId, opts = {}) {
-        return !!((await this.parse(opts)).indices[seqId] || {}).binIndex;
+        var _a;
+        const idx = await this.parse(opts);
+        return !!((_a = idx.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
     }
 }
 //# sourceMappingURL=indexFile.js.map

package/esm/indexFile.js.map

@@ -1 +1 @@
-{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAoBA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMM,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,6DAA6D;QAC7D,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACnD,OAAO,IAAI,CAAA;IACb,CAAC;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE;YACd,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;SACf;aAAM;YACL,OAAO,aAAa,CAAA;SACrB;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;QAC/C,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAA;IACnE,CAAC;CACF"}
+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAoBA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMM,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7D,OAAO,IAAI,CAAA;IACb,CAAC;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;;QAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAClC,OAAO,CAAC,CAAC,CAAA,MAAA,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,QAAQ,CAAA,CAAA;IACvC,CAAC;CACF"}

package/esm/tabixIndexedFile.d.ts

@@ -48,12 +48,10 @@ export default class TabixIndexedFile {
      * @param opts callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
      * @returns promise that is resolved when the whole read is finished, rejected on error
      */
-    getLines(refName: string, start: number, end: number, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
+    getLines(refName: string, s: number | undefined, e: number | undefined, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
     getMetadata(opts?: Options): Promise<{
         [key: string]: any;
-        refNameToId: {
-            [key: string]: number;
-        };
+        refNameToId: Record<string, number>;
         refIdToName: string[];
         metaChar: string | null;
         columnNumbers: {

package/esm/tabixIndexedFile.js

@@ -6,7 +6,7 @@ import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
 import { checkAbortSignal } from './util';
 import TBI from './tbi';
 import CSI from './csi';
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf-8') : undefined;
+const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 function timeout(time) {
     return new Promise(resolve => setTimeout(resolve, time));
 }
@@ -82,11 +82,12 @@ export default class TabixIndexedFile {
      * @param opts callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
      * @returns promise that is resolved when the whole read is finished, rejected on error
      */
-    async getLines(refName, start, end, opts) {
+    async getLines(refName, s, e, opts) {
+        var _a;
         let signal;
         let options = {};
         let callback;
-        if (typeof opts === 'undefined') {
+        if (opts === undefined) {
             throw new TypeError('line callback must be provided');
         }
         if (typeof opts === 'function') {
@@ -95,6 +96,7 @@ export default class TabixIndexedFile {
         else {
             options = opts;
             callback = opts.lineCallback;
+            signal = opts.signal;
         }
         if (refName === undefined) {
             throw new TypeError('must provide a reference sequence name');
@@ -104,12 +106,8 @@ export default class TabixIndexedFile {
         }
         const metadata = await this.index.getMetadata(options);
         checkAbortSignal(signal);
-        if (!start) {
-            start = 0;
-        }
-        if (!end) {
-            end = metadata.maxRefLength;
-        }
+        const start = s !== null && s !== void 0 ? s : 0;
+        const end = e !== null && e !== void 0 ? e : metadata.maxRefLength;
         if (!(start <= end)) {
             throw new TypeError('invalid start and end coordinates. start must be less than or equal to end');
         }
@@ -120,18 +118,17 @@ export default class TabixIndexedFile {
         checkAbortSignal(signal);
         // check the chunks for any that are over the size limit.  if
         // any are, don't fetch any of them
-        for (let i = 0; i < chunks.length; i += 1) {
-            const size = chunks[i].fetchedSize();
+        for (const chunk of chunks) {
+            const size = chunk.fetchedSize();
             if (size > this.chunkSizeLimit) {
                 throw new Error(`Too much data. Chunk size ${size.toLocaleString()} bytes exceeds chunkSizeLimit of ${this.chunkSizeLimit.toLocaleString()}.`);
             }
         }
         // now go through each chunk and parse and filter the lines out of it
         let last = Date.now();
-        for (let chunkNum = 0; chunkNum < chunks.length; chunkNum += 1) {
+        for (const c of chunks) {
             let previousStartCoordinate;
-            const c = chunks[chunkNum];
-            const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c);
+            const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c, signal);
             checkAbortSignal(signal);
             let blockStart = 0;
             let pos = 0;
@@ -141,7 +138,7 @@ export default class TabixIndexedFile {
                     break;
                 }
                 const b = buffer.slice(blockStart, n);
-                const line = (decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString();
+                const line = (_a = decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) !== null && _a !== void 0 ? _a : b.toString();
                 if (dpositions) {
                     while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
                     pos--;
@@ -201,17 +198,8 @@ export default class TabixIndexedFile {
         const maxFetch = ((firstDataLine === null || firstDataLine === void 0 ? void 0 : firstDataLine.blockPosition) || 0) + maxBlockSize;
         // TODO: what if we don't have a firstDataLine, and the header
         // actually takes up more than one block? this case is not covered here
-        let bytes = await this._readRegion(0, maxFetch, opts);
-        checkAbortSignal(opts.signal);
-        try {
-            bytes = await unzip(bytes);
-        }
-        catch (e) {
-            console.error(e);
-            throw new Error(
-            //@ts-ignore
-            `error decompressing block ${e.code} at 0 (length ${maxFetch}) ${e}`);
-        }
+        const buf = await this._readRegion(0, maxFetch, opts);
+        const bytes = await unzip(buf);
         // trim off lines after the last non-meta line
         if (metaChar) {
             // trim backward from the end
@@ -226,7 +214,7 @@ export default class TabixIndexedFile {
                     lastNewline = i;
                 }
             }
-            bytes = bytes.slice(0, lastNewline + 1);
+            return bytes.slice(0, lastNewline + 1);
         }
         return bytes;
     }
@@ -262,7 +250,7 @@ export default class TabixIndexedFile {
     checkLine(metadata, regionRefName, regionStart, regionEnd, line) {
         const { columnNumbers, metaChar, coordinateType, format } = metadata;
         // skip meta lines
-        if (line.charAt(0) === metaChar) {
+        if (metaChar && line.startsWith(metaChar)) {
             return { overlaps: false };
         }
         // check ref/start/end using column metadata from index
@@ -315,14 +303,10 @@ export default class TabixIndexedFile {
                     refSeq = line.slice(currentColumnStart, i);
                 }
                 else if (currentColumnNumber === end) {
-                    let endCoordinate;
                     // this will never match if there is no end column
-                    if (format === 'VCF') {
-                        endCoordinate = this._getVcfEnd(startCoordinate, refSeq, line.slice(currentColumnStart, i));
-                    }
-                    else {
-                        endCoordinate = parseInt(line.slice(currentColumnStart, i), 10);
-                    }
+                    const endCoordinate = format === 'VCF'
+                        ? this._getVcfEnd(startCoordinate, refSeq, line.slice(currentColumnStart, i))
+                        : parseInt(line.slice(currentColumnStart, i), 10);
                     if (endCoordinate <= regionStart) {
                         return { overlaps: false };
                     }
@@ -338,12 +322,12 @@ export default class TabixIndexedFile {
     }
     _getVcfEnd(startCoordinate, refSeq, info) {
         let endCoordinate = startCoordinate + refSeq.length;
-        // ignore TRA features as they specify CHR2 and END
-        // as being on a different chromosome
-        // if CHR2 is on the same chromosome, still ignore it
-        // because there should be another pairwise feature
-        // at the end of this one
-        const isTRA = info.indexOf('SVTYPE=TRA') !== -1;
+        // ignore TRA features as they specify CHR2 and END as being on a different
+        // chromosome
+        //
+        // if CHR2 is on the same chromosome, still ignore it because there should
+        // be another pairwise feature at the end of this one
+        const isTRA = info.includes('SVTYPE=TRA');
         if (info[0] !== '.' && !isTRA) {
             let prevChar = ';';
             for (let j = 0; j < info.length; j += 1) {
@@ -384,12 +368,7 @@ export default class TabixIndexedFile {
         // fetch the uncompressed data, uncompress carefully a block at a time,
         // and stop when done
         const data = await this._readRegion(c.minv.blockPosition, c.fetchedSize(), opts);
-        try {
-            return unzipChunkSlice(data, c);
-        }
-        catch (e) {
-            throw new Error(`error decompressing c ${c.toString()} ${e}`);
-        }
+        return unzipChunkSlice(data, c);
     }
 }
 //# sourceMappingURL=tabixIndexedFile.js.map

package/esm/tabixIndexedFile.js.map

@@ -1 +1 @@
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package/esm/tbi.d.ts

@@ -7,9 +7,7 @@ export default class TabixIndex extends IndexFile {
     lineCount(refName: string, opts?: Options): Promise<any>;
     _parse(opts?: Options): Promise<{
         indices: {
-            binIndex: {
-                [key: number]: Chunk[];
-            };
+            binIndex: Record<number, Chunk[]>;
             linearIndex: any[];
             stats: {
                 lineCount: number;
@@ -28,18 +26,14 @@ export default class TabixIndex extends IndexFile {
         coordinateType: string;
         format: string;
         refIdToName: string[];
-        refNameToId: {
-            [key: string]: number;
-        };
+        refNameToId: Record<string, number>;
         maxBlockSize: number;
     }>;
     parsePseudoBin(bytes: Buffer, offset: number): {
         lineCount: number;
     };
     _parseNameBytes(namesBytes: Buffer): {
-        refNameToId: {
-            [key: string]: number;
-        };
+        refNameToId: Record<string, number>;
         refIdToName: string[];
     };
     blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;

package/esm/tbi.js

@@ -189,9 +189,8 @@ export default class TabixIndex extends IndexFile {
         for (const [start, end] of overlappingBins) {
             for (let bin = start; bin <= end; bin++) {
                 if (ba.binIndex[bin]) {
-                    const binChunks = ba.binIndex[bin];
-                    for (let c = 0; c < binChunks.length; ++c) {
-                        chunks.push(new Chunk(binChunks[c].minv, binChunks[c].maxv, bin));
+                    for (const c of ba.binIndex[bin]) {
+                        chunks.push(new Chunk(c.minv, c.maxv, bin));
                     }
                 }
             }

package/esm/tbi.js.map

@@ -1 +1 @@
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