@gmod/tabix 3.3.9 → 3.4.1

package/dist/tabixIndexedFile.d.ts

@@ -5,24 +5,22 @@ type GetLinesCallback = (line: string, fileOffset: number, start: number, end: n
 interface GetLinesOpts {
     signal?: AbortSignal;
     lineCallback: GetLinesCallback;
+    /**
+     * Called as the compressed data blocks covering the query are fetched, with
+     * cumulative downloaded bytes and the total bytes to fetch. Reported at block
+     * granularity (one tick per chunk, including instant ticks for cache hits),
+     * which is the natural unit since chunk byte sizes are known up front from
+     * the index. Lets callers render a determinate download progress bar.
+     */
+    onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
 }
+/**
+ * Reads Tabix-indexed files (bgzipped), supporting both .tbi and .csi index formats.
+ */
 export default class TabixIndexedFile {
     private filehandle;
     private index;
     private chunkCache;
-    /**
-     * @param {object} args
-     * @param {string} [args.path]
-     * @param {object} [args.filehandle]
-     * @param {string} [args.url]
-     * @param {string} [args.tbiPath]
-     * @param {string} [args.tbiUrl]
-     * @param {object} [args.tbiFilehandle]
-     * @param {string} [args.csiPath]
-     * @param {string} [args.csiUrl]
-     * @param {object} [args.csiFilehandle]
-     * @param {number} [args.chunkCacheSize]
-     */
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, }: {
         path?: string;
         filehandle?: GenericFilehandle;
@@ -46,13 +44,13 @@ export default class TabixIndexedFile {
         end: number;
     }[], opts?: Options): Promise<number>;
     /**
-     * @param {string} refName name of the reference sequence
-     * @param {number|undefined} start start of the region (0-based half-open)
-     * @param {number|undefined} end end of the region (0-based half-open)
-     * @param {GetLinesOpts|GetLinesCallback} opts callback invoked for each line, or an options object with `lineCallback` and optional `signal`
-     * @returns {Promise} promise that is resolved when the whole read is finished, rejected on error
+     * @param refName name of the reference sequence
+     * @param s start of the region (0-based half-open)
+     * @param e end of the region (0-based half-open)
+     * @param opts callback invoked for each line, or an options object with `lineCallback` and optional `signal`
      */
     getLines(refName: string, s: number | undefined, e: number | undefined, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
+    /** @internal */
     getMetadata(opts?: Options): Promise<{
         refNameToId: Record<string, number>;
         refIdToName: string[];
@@ -77,12 +75,9 @@ export default class TabixIndexedFile {
     getHeaderBuffer(opts?: Options): Promise<Uint8Array<ArrayBufferLike>>;
     getHeader(opts?: Options): Promise<string>;
     getReferenceSequenceNames(opts?: Options): Promise<string[]>;
-    /**
-     * return the number of data lines in the given reference sequence
-     * @param {string} refName reference sequence name
-     * @returns {number} number of data lines present on that reference sequence
-     */
+    /** @param refName reference sequence name */
     lineCount(refName: string, opts?: Options): Promise<number>;
+    /** @internal */
     readChunk(c: Chunk, opts?: Options): Promise<{
         buffer: Uint8Array<ArrayBufferLike>;
         cpositions: number[];

package/dist/tabixIndexedFile.js

@@ -85,23 +85,13 @@ function parseIntFromBytes(buffer, start, end) {
     }
     return val;
 }
+/**
+ * Reads Tabix-indexed files (bgzipped), supporting both .tbi and .csi index formats.
+ */
 class TabixIndexedFile {
     filehandle;
     index;
     chunkCache;
-    /**
-     * @param {object} args
-     * @param {string} [args.path]
-     * @param {object} [args.filehandle]
-     * @param {string} [args.url]
-     * @param {string} [args.tbiPath]
-     * @param {string} [args.tbiUrl]
-     * @param {object} [args.tbiFilehandle]
-     * @param {string} [args.csiPath]
-     * @param {string} [args.csiUrl]
-     * @param {object} [args.csiFilehandle]
-     * @param {number} [args.chunkCacheSize]
-     */
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = 5 * 2 ** 20, }) {
         this.filehandle = resolveFilehandle(filehandle, path, url);
         if (tbiFilehandle) {
@@ -156,16 +146,16 @@ class TabixIndexedFile {
         return bytes;
     }
     /**
-     * @param {string} refName name of the reference sequence
-     * @param {number|undefined} start start of the region (0-based half-open)
-     * @param {number|undefined} end end of the region (0-based half-open)
-     * @param {GetLinesOpts|GetLinesCallback} opts callback invoked for each line, or an options object with `lineCallback` and optional `signal`
-     * @returns {Promise} promise that is resolved when the whole read is finished, rejected on error
+     * @param refName name of the reference sequence
+     * @param s start of the region (0-based half-open)
+     * @param e end of the region (0-based half-open)
+     * @param opts callback invoked for each line, or an options object with `lineCallback` and optional `signal`
      */
     async getLines(refName, s, e, opts) {
         let signal;
         let options = {};
         let callback;
+        let onProgress;
         if (typeof opts === 'function') {
             callback = opts;
         }
@@ -173,6 +163,7 @@ class TabixIndexedFile {
             options = opts;
             callback = opts.lineCallback;
             signal = opts.signal;
+            onProgress = opts.onProgress;
         }
         const metadata = await this.index.getMetadata(options);
         const start = s ?? 0;
@@ -197,8 +188,16 @@ class TabixIndexedFile {
         // tabs[N] holds the byte offset of the N-th tab on the current line; with
         // the sentinel tabs[0] = blockStart - 1, column N spans tabs[N-1]+1..tabs[N]
         const tabs = new Int32Array(maxColumn + 1);
+        let totalBytes = 0;
+        for (const c of chunks) {
+            totalBytes += c.fetchedSize();
+        }
+        let downloadedBytes = 0;
+        onProgress?.(0, totalBytes);
         for (const c of chunks) {
             const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c, signal);
+            downloadedBytes += c.fetchedSize();
+            onProgress?.(downloadedBytes, totalBytes);
             const minvDataPosition = c.minv.dataPosition;
             let blockStart = 0;
             let pos = 0;
@@ -270,6 +269,7 @@ class TabixIndexedFile {
             }
         }
     }
+    /** @internal */
     async getMetadata(opts = {}) {
         return this.index.getMetadata(opts);
     }
@@ -305,14 +305,11 @@ class TabixIndexedFile {
         const metadata = await this.getMetadata(opts);
         return metadata.refIdToName;
     }
-    /**
-     * return the number of data lines in the given reference sequence
-     * @param {string} refName reference sequence name
-     * @returns {number} number of data lines present on that reference sequence
-     */
+    /** @param refName reference sequence name */
     async lineCount(refName, opts = {}) {
         return this.index.lineCount(refName, opts);
     }
+    /** @internal */
     async readChunk(c, opts = {}) {
         const ret = await this.filehandle.read(c.fetchedSize(), c.minv.blockPosition, opts);
         return (0, bgzf_filehandle_1.unzipChunkSlice)(ret, c);

package/dist/tabixIndexedFile.js.map

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package/dist/tbi.d.ts

@@ -3,6 +3,7 @@ import IndexFile from './indexFile.ts';
 import type { Options, RefIndex } from './indexFile.ts';
 import type VirtualOffset from './virtualOffset.ts';
 export default class TabixIndex extends IndexFile {
+    /** @internal */
     _parse(opts?: Options): Promise<{
         indices: (refId: number) => RefIndex | undefined;
         metaChar: string | undefined;

package/dist/tbi.js

@@ -26,9 +26,12 @@ function reg2bins(beg, end) {
     ];
 }
 class TabixIndex extends indexFile_ts_1.default {
-    // fetch and parse the index
+    /** @internal */
     async _parse(opts = {}) {
-        const buf = await this.filehandle.readFile({ signal: opts.signal });
+        const buf = await this.filehandle.readFile({
+            signal: opts.signal,
+            onProgress: opts.onProgress,
+        });
         const bytes = (await (0, bgzf_filehandle_1.unzip)(buf));
         const dataView = new DataView(bytes.buffer);
         if (dataView.getUint32(0, true) !== TBI_MAGIC) {

package/dist/tbi.js.map

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

@@ -10,7 +10,9 @@ export default class CSI extends IndexFile {
     constructor(args: {
         filehandle: GenericFilehandle;
     });
+    /** @internal */
     indexCov(): void;
+    /** @internal */
     _parse(opts?: Options): Promise<{
         csi: boolean;
         refCount: number;
@@ -54,8 +56,6 @@ export default class CSI extends IndexFile {
         format: string;
     }>;
     blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
-    /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     */
+    /** @internal */
     reg2bins(beg: number, end: number): (readonly [number, number])[];
 }

package/esm/csi.js

@@ -23,11 +23,16 @@ export default class CSI extends IndexFile {
         this.depth = 0;
         this.minShift = 0;
     }
+    /** @internal */
     indexCov() {
         throw new Error('CSI indexes do not support indexcov');
     }
+    /** @internal */
     async _parse(opts = {}) {
-        const buf = await this.filehandle.readFile({ signal: opts.signal });
+        const buf = await this.filehandle.readFile({
+            signal: opts.signal,
+            onProgress: opts.onProgress,
+        });
         const bytes = (await unzip(buf));
         const dataView = new DataView(bytes.buffer);
         const magic = dataView.getUint32(0, true);
@@ -154,9 +159,7 @@ export default class CSI extends IndexFile {
         }
         return optimizeChunks(chunks);
     }
-    /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     */
+    /** @internal */
     reg2bins(beg, end) {
         const maxPos = 2 ** (this.minShift + this.depth * 3);
         if (end > maxPos) {

package/esm/csi.js.map

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

@@ -3,6 +3,12 @@ import type VirtualOffset from './virtualOffset.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export interface Options {
     signal?: AbortSignal;
+    /**
+     * Called as the index (.tbi/.csi) is downloaded, with cumulative downloaded
+     * bytes and the total. The index is a whole-file read, so this streams real
+     * byte progress. Lets callers show a determinate "downloading index" bar.
+     */
+    onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
 }
 export interface RefIndex {
     binIndex: Record<number, Chunk[]>;
@@ -40,7 +46,9 @@ export default abstract class IndexFile {
         filehandle: GenericFilehandle;
     });
     protected abstract _parse(opts: Options): Promise<IndexData>;
+    /** @internal */
     lineCount(refName: string, opts?: Options): Promise<number>;
+    /** @internal */
     getMetadata(opts?: Options): Promise<{
         refNameToId: Record<string, number>;
         refIdToName: string[];
@@ -62,7 +70,10 @@ export default abstract class IndexFile {
         csiVersion?: number;
         depth?: number;
     }>;
+    /** @internal */
     abstract blocksForRange(refName: string, start: number, end: number, opts: Options): Promise<Chunk[]>;
+    /** @internal */
     parse(opts?: Options): Promise<IndexData>;
+    /** @internal */
     hasRefSeq(seqId: number, opts?: Options): Promise<boolean>;
 }

package/esm/indexFile.js

@@ -4,6 +4,7 @@ export default class IndexFile {
     constructor({ filehandle }) {
         this.filehandle = filehandle;
     }
+    /** @internal */
     async lineCount(refName, opts = {}) {
         const indexData = await this.parse(opts);
         const refId = indexData.refNameToId[refName];
@@ -12,10 +13,12 @@ export default class IndexFile {
         }
         return indexData.indices(refId)?.stats?.lineCount ?? -1;
     }
+    /** @internal */
     async getMetadata(opts = {}) {
         const { indices: _indices, ...rest } = await this.parse(opts);
         return rest;
     }
+    /** @internal */
     async parse(opts = {}) {
         this.parseP ??= this._parse(opts).catch((error) => {
             this.parseP = undefined;
@@ -23,6 +26,7 @@ export default class IndexFile {
         });
         return this.parseP;
     }
+    /** @internal */
     async hasRefSeq(seqId, opts = {}) {
         const idx = await this.parse(opts);
         return !!idx.indices(seqId)?.binIndex;

package/esm/indexFile.js.map

@@ -1 +1 @@
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+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAuCA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAC9B,UAAU,CAAmB;IAC5B,MAAM,CAAqB;IAEnC,YAAY,EAAE,UAAU,EAAqC;QAC3D,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;IAC9B,CAAC;IAID,gBAAgB;IACT,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACxD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAC,CAAA;IACzD,CAAC;IAED,gBAAgB;IACT,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;IAUD,gBAAgB;IAChB,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAc,EAAE,EAAE;YACzD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,MAAM,KAAK,CAAA;QACb,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,gBAAgB;IAChB,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,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IACvC,CAAC;CACF"}

package/esm/tabixIndexedFile.d.ts

@@ -5,24 +5,22 @@ type GetLinesCallback = (line: string, fileOffset: number, start: number, end: n
 interface GetLinesOpts {
     signal?: AbortSignal;
     lineCallback: GetLinesCallback;
+    /**
+     * Called as the compressed data blocks covering the query are fetched, with
+     * cumulative downloaded bytes and the total bytes to fetch. Reported at block
+     * granularity (one tick per chunk, including instant ticks for cache hits),
+     * which is the natural unit since chunk byte sizes are known up front from
+     * the index. Lets callers render a determinate download progress bar.
+     */
+    onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
 }
+/**
+ * Reads Tabix-indexed files (bgzipped), supporting both .tbi and .csi index formats.
+ */
 export default class TabixIndexedFile {
     private filehandle;
     private index;
     private chunkCache;
-    /**
-     * @param {object} args
-     * @param {string} [args.path]
-     * @param {object} [args.filehandle]
-     * @param {string} [args.url]
-     * @param {string} [args.tbiPath]
-     * @param {string} [args.tbiUrl]
-     * @param {object} [args.tbiFilehandle]
-     * @param {string} [args.csiPath]
-     * @param {string} [args.csiUrl]
-     * @param {object} [args.csiFilehandle]
-     * @param {number} [args.chunkCacheSize]
-     */
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, }: {
         path?: string;
         filehandle?: GenericFilehandle;
@@ -46,13 +44,13 @@ export default class TabixIndexedFile {
         end: number;
     }[], opts?: Options): Promise<number>;
     /**
-     * @param {string} refName name of the reference sequence
-     * @param {number|undefined} start start of the region (0-based half-open)
-     * @param {number|undefined} end end of the region (0-based half-open)
-     * @param {GetLinesOpts|GetLinesCallback} opts callback invoked for each line, or an options object with `lineCallback` and optional `signal`
-     * @returns {Promise} promise that is resolved when the whole read is finished, rejected on error
+     * @param refName name of the reference sequence
+     * @param s start of the region (0-based half-open)
+     * @param e end of the region (0-based half-open)
+     * @param opts callback invoked for each line, or an options object with `lineCallback` and optional `signal`
      */
     getLines(refName: string, s: number | undefined, e: number | undefined, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
+    /** @internal */
     getMetadata(opts?: Options): Promise<{
         refNameToId: Record<string, number>;
         refIdToName: string[];
@@ -77,12 +75,9 @@ export default class TabixIndexedFile {
     getHeaderBuffer(opts?: Options): Promise<Uint8Array<ArrayBufferLike>>;
     getHeader(opts?: Options): Promise<string>;
     getReferenceSequenceNames(opts?: Options): Promise<string[]>;
-    /**
-     * return the number of data lines in the given reference sequence
-     * @param {string} refName reference sequence name
-     * @returns {number} number of data lines present on that reference sequence
-     */
+    /** @param refName reference sequence name */
     lineCount(refName: string, opts?: Options): Promise<number>;
+    /** @internal */
     readChunk(c: Chunk, opts?: Options): Promise<{
         buffer: Uint8Array<ArrayBufferLike>;
         cpositions: number[];

package/esm/tabixIndexedFile.js

@@ -80,23 +80,13 @@ function parseIntFromBytes(buffer, start, end) {
     }
     return val;
 }
+/**
+ * Reads Tabix-indexed files (bgzipped), supporting both .tbi and .csi index formats.
+ */
 export default class TabixIndexedFile {
     filehandle;
     index;
     chunkCache;
-    /**
-     * @param {object} args
-     * @param {string} [args.path]
-     * @param {object} [args.filehandle]
-     * @param {string} [args.url]
-     * @param {string} [args.tbiPath]
-     * @param {string} [args.tbiUrl]
-     * @param {object} [args.tbiFilehandle]
-     * @param {string} [args.csiPath]
-     * @param {string} [args.csiUrl]
-     * @param {object} [args.csiFilehandle]
-     * @param {number} [args.chunkCacheSize]
-     */
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = 5 * 2 ** 20, }) {
         this.filehandle = resolveFilehandle(filehandle, path, url);
         if (tbiFilehandle) {
@@ -151,16 +141,16 @@ export default class TabixIndexedFile {
         return bytes;
     }
     /**
-     * @param {string} refName name of the reference sequence
-     * @param {number|undefined} start start of the region (0-based half-open)
-     * @param {number|undefined} end end of the region (0-based half-open)
-     * @param {GetLinesOpts|GetLinesCallback} opts callback invoked for each line, or an options object with `lineCallback` and optional `signal`
-     * @returns {Promise} promise that is resolved when the whole read is finished, rejected on error
+     * @param refName name of the reference sequence
+     * @param s start of the region (0-based half-open)
+     * @param e end of the region (0-based half-open)
+     * @param opts callback invoked for each line, or an options object with `lineCallback` and optional `signal`
      */
     async getLines(refName, s, e, opts) {
         let signal;
         let options = {};
         let callback;
+        let onProgress;
         if (typeof opts === 'function') {
             callback = opts;
         }
@@ -168,6 +158,7 @@ export default class TabixIndexedFile {
             options = opts;
             callback = opts.lineCallback;
             signal = opts.signal;
+            onProgress = opts.onProgress;
         }
         const metadata = await this.index.getMetadata(options);
         const start = s ?? 0;
@@ -192,8 +183,16 @@ export default class TabixIndexedFile {
         // tabs[N] holds the byte offset of the N-th tab on the current line; with
         // the sentinel tabs[0] = blockStart - 1, column N spans tabs[N-1]+1..tabs[N]
         const tabs = new Int32Array(maxColumn + 1);
+        let totalBytes = 0;
+        for (const c of chunks) {
+            totalBytes += c.fetchedSize();
+        }
+        let downloadedBytes = 0;
+        onProgress?.(0, totalBytes);
         for (const c of chunks) {
             const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c, signal);
+            downloadedBytes += c.fetchedSize();
+            onProgress?.(downloadedBytes, totalBytes);
             const minvDataPosition = c.minv.dataPosition;
             let blockStart = 0;
             let pos = 0;
@@ -265,6 +264,7 @@ export default class TabixIndexedFile {
             }
         }
     }
+    /** @internal */
     async getMetadata(opts = {}) {
         return this.index.getMetadata(opts);
     }
@@ -300,14 +300,11 @@ export default class TabixIndexedFile {
         const metadata = await this.getMetadata(opts);
         return metadata.refIdToName;
     }
-    /**
-     * return the number of data lines in the given reference sequence
-     * @param {string} refName reference sequence name
-     * @returns {number} number of data lines present on that reference sequence
-     */
+    /** @param refName reference sequence name */
     async lineCount(refName, opts = {}) {
         return this.index.lineCount(refName, opts);
     }
+    /** @internal */
     async readChunk(c, opts = {}) {
         const ret = await this.filehandle.read(c.fetchedSize(), c.minv.blockPosition, opts);
         return unzipChunkSlice(ret, c);