@gmod/tabix 3.5.2 → 3.5.4

package/README.md

@@ -20,13 +20,13 @@ import { TabixIndexedFile } from '@gmod/tabix'
 const file = new TabixIndexedFile({ path: 'file.vcf.gz' })
 
 // CSI index
-const file = new TabixIndexedFile({
+const csi = new TabixIndexedFile({
   path: 'file.vcf.gz',
   csiPath: 'file.vcf.gz.csi',
 })
 
 // Remote files
-const file = new TabixIndexedFile({
+const remote = new TabixIndexedFile({
   url: 'https://example.com/file.vcf.gz',
   tbiUrl: 'https://example.com/file.vcf.gz.tbi',
 })
@@ -34,7 +34,7 @@ const file = new TabixIndexedFile({
 // Or with a filehandle from generic-filehandle2
 import { RemoteFile } from 'generic-filehandle2'
 
-const file = new TabixIndexedFile({
+const custom = new TabixIndexedFile({
   filehandle: new RemoteFile('https://example.com/file.vcf.gz'),
   tbiFilehandle: new RemoteFile('https://example.com/file.vcf.gz.tbi'),
 })
@@ -59,21 +59,34 @@ await file.getLines('chr1', 200, 300, (line, fileOffset, start, end) => {
 })
 ```
 
-Pass an options object to use an `AbortSignal`:
+Pass an options object instead of a bare callback to abort the query or track
+download progress:
 
 ```typescript
 const aborter = new AbortController()
 await file.getLines('chr1', 200, 300, {
   lineCallback: (line, fileOffset, start, end) => lines.push(line),
   signal: aborter.signal,
+  onProgress: (bytesDownloaded, totalBytes) => {
+    console.log(`${bytesDownloaded}/${totalBytes}`)
+  },
 })
 ```
 
+`onProgress` ticks once per compressed block, including instant ticks for cache
+hits, and `totalBytes` is known up front from the index — enough for a
+determinate progress bar.
+
 Notes:
 
 - Meta/comment lines are skipped
 - Line strings have no trailing whitespace
 - Pass `undefined` for `end` to read to the end of the contig
+- A `refName` that is not in the index yields no lines and no error, so a
+  `chr1`/`1` naming mismatch looks like an empty region. Check against
+  [`getReferenceSequenceNames`](#getreferencesequencenamesopts-promisestring) if
+  a query comes back unexpectedly empty
+- `start > end` throws a `TypeError`; `start === end` returns without reading
 
 ### Without NPM (CDN)
 
@@ -81,7 +94,9 @@ Notes:
 <script src="https://unpkg.com/@gmod/tabix/dist/tabix-bundle.js"></script>
 ```
 
-See [example/index.html](example/index.html) for a working demo.
+See [example/index.html](example/index.html) for a working demo. It fetches the
+VCF over HTTP, so serve the directory (e.g. `npx serve example`) rather than
+opening the file directly.
 
 ## API
 
@@ -98,27 +113,56 @@ See [example/index.html](example/index.html) for a working demo.
 | `csiPath`        | `string?`            | CSI index path                                                                              |
 | `csiUrl`         | `string?`            | CSI index URL                                                                               |
 | `csiFilehandle`  | `GenericFilehandle?` | CSI index filehandle                                                                        |
-| `chunkCacheSize` | `number?`            | Chunk LRU cache size in bytes (default 5 MiB)                                               |
+| `chunkCacheSize` | `number?`            | Chunk LRU cache budget, in _decompressed_ bytes (default 100 MiB)                           |
 
 ### `getLines(refName, start, end, opts)`
 
-Calls `opts` (or `opts.lineCallback`) for each line overlapping `[start, end)`.
+Calls the line callback for each line overlapping `[start, end)`. `start`
+defaults to `0` and `end` to the end of the contig when `undefined`. `opts` is
+either the callback itself or an object:
 
-Callback signature:
-`(line: string, fileOffset: number, start: number, end: number) => void`
+| Option         | Type                                                     | Description                             |
+| -------------- | -------------------------------------------------------- | --------------------------------------- |
+| `lineCallback` | `(line, fileOffset, start, end) => void`                 | Required                                |
+| `signal`       | `AbortSignal?`                                           | Aborts the in-flight reads              |
+| `onProgress`   | `(bytesDownloaded: number, totalBytes?: number) => void` | Called as compressed blocks are fetched |
 
 ### `getHeader(opts?): Promise<string>`
 
-Returns all comment/meta lines before the first data line as a string.
+Returns all comment/meta lines before the first data line as a string, matching
+what `tabix -H` prints. A header row that is not commented is therefore not
+included, even when the index counted it as a line to skip — see
+`getSkippedLines`.
 
 ### `getHeaderBuffer(opts?): Promise<Uint8Array>`
 
 Returns the header as raw bytes.
 
+### `getSkippedLines(opts?): Promise<string[]>`
+
+Returns the leading lines the index says to skip (`tabix -S N`), or `[]` when it
+records none. This is where a file whose header row is not commented keeps it,
+which PLINK `.ld`, bedGraph and BED deflines routinely are.
+
+Separate from `getHeader` because htslib treats the two differently: a line is
+not data when the index's skip count covers it **or** it starts with the meta
+character, but `tabix -H` prints only the latter.
+
+### `getHeaderLines(opts?): Promise<string[]>`
+
+Returns the file's header lines however the file keeps them: the commented block
+when there is one, and otherwise the rows the index counted. Empty lines are
+dropped.
+
+This is usually the one you want. Reading `getHeader` alone cannot tell a file
+that has no header from one whose header is not commented — both come back as
+the empty string — so callers fall back to an assumed column layout and quietly
+mis-name columns. Both forms are parsed from a single read of the file's leading
+blocks, which is also shared with `getHeader` and `getSkippedLines`.
+
 ### `getReferenceSequenceNames(opts?): Promise<string[]>`
 
-Returns reference sequence names in index order. `renameRefSeqs` is not applied
-to these names.
+Returns reference sequence names in index order.
 
 ### `lineCount(refName, opts?): Promise<number>`
 
@@ -130,14 +174,9 @@ reference is not in the index.
 Estimates the compressed byte size of index chunks covering the given regions.
 Useful for deciding whether a request is too large before calling `getLines`.
 
-## Publishing
-
-[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub
-Actions.
+## Contributing
 
-```bash
-pnpm version patch  # or minor/major
-```
+See [CONTRIBUTING.md](CONTRIBUTING.md) for development and release steps.
 
 ## Academic Use
 

package/dist/csi.d.ts

@@ -1,11 +1,7 @@
-import Chunk from './chunk.ts';
 import IndexFile from './indexFile.ts';
-import type { Options, RefIndex } from './indexFile.ts';
+import type { IndexData, Options, RefIndex } from './indexFile.ts';
 import type VirtualOffset from './virtualOffset.ts';
 export default class CSI extends IndexFile {
-    private maxBinNumber;
-    private depth;
-    private minShift;
     /** @internal */
     _parse(opts?: Options): Promise<{
         csi: boolean;
@@ -14,6 +10,7 @@ export default class CSI extends IndexFile {
         firstDataLine: VirtualOffset | undefined;
         csiVersion: number;
         indices: (refId: number) => RefIndex | undefined;
+        minShift: number;
         depth: number;
         maxBinNumber: number;
         maxRefLength: number;
@@ -35,6 +32,7 @@ export default class CSI extends IndexFile {
         firstDataLine: VirtualOffset | undefined;
         csiVersion: number;
         indices: (refId: number) => RefIndex | undefined;
+        minShift: number;
         depth: number;
         maxBinNumber: number;
         maxRefLength: number;
@@ -49,7 +47,6 @@ export default class CSI extends IndexFile {
         coordinateType: string;
         format: string;
     }>;
-    blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
     /**
      * CSI's equivalent of the BAI/TBI linear index: the loffset of the deepest
      * indexed bin covering `beg` is the earliest virtual offset any record
@@ -57,7 +54,6 @@ export default class CSI extends IndexFile {
      * Walks leaf -> previous sibling -> parent until an indexed bin is found.
      * SYNC: htslib hts_itr_query min_off computation
      */
-    private minOffset;
-    /** @internal */
-    reg2bins(beg: number, end: number): (readonly [number, number])[];
+    protected lowestOffset(ref: RefIndex, beg: number, { minShift, depth }: IndexData): VirtualOffset | undefined;
+    protected reg2bins(beg: number, end: number, { minShift, depth, maxBinNumber }: IndexData): (readonly [number, number])[];
 }

package/dist/csi.js

@@ -3,7 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const chunk_ts_1 = __importDefault(require("./chunk.js"));
 const indexFile_ts_1 = __importDefault(require("./indexFile.js"));
 const util_ts_1 = require("./util.js");
@@ -19,17 +18,9 @@ function rshift(num, bits) {
     return Math.floor(num / 2 ** bits);
 }
 class CSI extends indexFile_ts_1.default {
-    maxBinNumber = 0;
-    depth = 0;
-    minShift = 0;
     /** @internal */
     async _parse(opts = {}) {
-        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, bytes.byteOffset, bytes.byteLength);
+        const { bytes, dataView } = await this.readIndexBytes(opts);
         const magic = dataView.getUint32(0, true);
         let csiVersion;
         if (magic === CSI1_MAGIC) {
@@ -41,11 +32,10 @@ class CSI extends indexFile_ts_1.default {
         else {
             throw new Error(`Not a CSI file (magic=${magic})`);
         }
-        this.minShift = dataView.getInt32(4, true);
-        this.depth = dataView.getInt32(8, true);
-        this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
-        const maxBinNumber = this.maxBinNumber;
-        const maxRefLength = 2 ** (this.minShift + this.depth * 3);
+        const minShift = dataView.getInt32(4, true);
+        const depth = dataView.getInt32(8, true);
+        const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7;
+        const maxRefLength = 2 ** (minShift + depth * 3);
         const auxLength = dataView.getInt32(12, true);
         const aux = auxLength >= 30
             ? (0, util_ts_1.parseAuxData)(bytes, 16)
@@ -123,40 +113,12 @@ class CSI extends indexFile_ts_1.default {
             firstDataLine,
             csiVersion,
             indices: (0, util_ts_1.memoizeByRefId)(getIndices),
-            depth: this.depth,
+            minShift,
+            depth,
             maxBinNumber,
             maxRefLength,
         };
     }
-    async blocksForRange(refName, min, max, opts = {}) {
-        if (min < 0) {
-            min = 0;
-        }
-        const indexData = await this.parse(opts);
-        const refId = indexData.refNameToId[refName];
-        if (refId === undefined) {
-            return [];
-        }
-        const ba = indexData.indices(refId);
-        if (!ba) {
-            return [];
-        }
-        // List of bin #s that overlap min, max
-        const overlappingBins = this.reg2bins(min, max);
-        const chunks = [];
-        // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
-        for (const [start, end] of overlappingBins) {
-            for (let bin = start; bin <= end; bin++) {
-                const binChunks = ba.binIndex[bin];
-                if (binChunks) {
-                    for (const c of binChunks) {
-                        chunks.push(c);
-                    }
-                }
-            }
-        }
-        return (0, util_ts_1.optimizeChunks)(chunks, this.minOffset(ba.loffsets, min));
-    }
     /**
      * CSI's equivalent of the BAI/TBI linear index: the loffset of the deepest
      * indexed bin covering `beg` is the earliest virtual offset any record
@@ -164,11 +126,12 @@ class CSI extends indexFile_ts_1.default {
      * Walks leaf -> previous sibling -> parent until an indexed bin is found.
      * SYNC: htslib hts_itr_query min_off computation
      */
-    minOffset(loffsets, beg) {
+    lowestOffset(ref, beg, { minShift, depth }) {
+        const { loffsets } = ref;
         let found;
         if (loffsets) {
             // first bin of the deepest level, i.e. (8**depth - 1) / 7
-            let bin = (lshift(1, 3 * this.depth) - 1) / 7 + rshift(beg, this.minShift);
+            let bin = (lshift(1, 3 * depth) - 1) / 7 + rshift(Math.max(beg, 0), minShift);
             while (found === undefined && bin > 0) {
                 found = loffsets[bin];
                 if (found === undefined) {
@@ -181,22 +144,22 @@ class CSI extends indexFile_ts_1.default {
         }
         return found;
     }
-    /** @internal */
-    reg2bins(beg, end) {
-        const maxPos = 2 ** (this.minShift + this.depth * 3);
+    reg2bins(beg, end, { minShift, depth, maxBinNumber }) {
+        beg = Math.max(beg, 0);
+        const maxPos = 2 ** (minShift + depth * 3);
         if (end > maxPos) {
             end = maxPos;
         }
         end -= 1;
         let l = 0;
         let t = 0;
-        let s = this.minShift + this.depth * 3;
+        let s = minShift + depth * 3;
         const bins = [];
-        for (; l <= this.depth; s -= 3, t += lshift(1, l * 3), l += 1) {
+        for (; l <= depth; s -= 3, t += lshift(1, l * 3), l += 1) {
             const b = t + rshift(beg, s);
             const e = t + rshift(end, s);
-            if (e - b + bins.length > this.maxBinNumber) {
-                throw new Error(`query ${beg}-${end} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);
+            if (e - b + bins.length > maxBinNumber) {
+                throw new Error(`query ${beg}-${end} is too large for current binning scheme (shift ${minShift}, depth ${depth}), try a smaller query or a coarser index binning scheme`);
             }
             bins.push([b, e]);
         }

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+{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,0DAA8B;AAC9B,kEAAsC;AACtC,uCAMkB;AAClB,yDAA8C;AAK9C,MAAM,UAAU,GAAG,UAAU,CAAA,CAAC,QAAQ;AACtC,MAAM,UAAU,GAAG,UAAU,CAAA,CAAC,QAAQ;AAEtC,gFAAgF;AAChF,wDAAwD;AACxD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IACxC,gBAAgB;IAChB,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;QAE3D,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACzC,IAAI,UAAU,CAAA;QACd,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,yBAAyB,KAAK,GAAG,CAAC,CAAA;QACpD,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC3C,MAAM,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACxC,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QACvD,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,QAAQ,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;QAChD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GACP,SAAS,IAAI,EAAE;YACb,CAAC,CAAC,IAAA,sBAAY,EAAC,KAAK,EAAE,EAAE,CAAC;YACzB,CAAC,CAAC;gBACE,WAAW,EAAE,EAAc;gBAC3B,WAAW,EAAE,EAA4B;gBACzC,QAAQ,EAAE,SAAS;gBACnB,aAAa,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE;gBAC3C,cAAc,EAAE,sBAAsB;gBACtC,MAAM,EAAE,SAAS;aAClB,CAAA;QACP,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,iEAAiE;QACjE,gFAAgF;QAChF,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAa,EAAE,CAAA;QAE5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA,CAAC,gDAAgD;gBAClE,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,IAAA,0BAAgB,EAAC,KAAK,EAAE,IAAI,EAAE,CAAC,EAAE,aAAa,CAAC,CAAA;oBAC/D,IAAI,IAAI,CAAC,CAAA,CAAC,UAAU;oBACpB,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,UAAU,CAAA;gBAC7B,CAAC;YACH,CAAC;QACH,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YAC5B,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,IAAI,GAAG,GAAG,KAAK,CAAA;YACf,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YAC7C,GAAG,IAAI,CAAC,CAAA;YACR,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,MAAM,QAAQ,GAAkC,EAAE,CAAA;YAClD,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;gBACzC,GAAG,IAAI,CAAC,CAAA;gBACR,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,KAAK,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,GAAG,GAAG,EAAE,CAAC,CAAA;oBACvC,GAAG,IAAI,EAAE,GAAG,EAAE,CAAA;gBAChB,CAAC;qBAAM,CAAC;oBACN,QAAQ,CAAC,GAAG,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,GAAG,CAAC,CAAA;oBACrC,GAAG,IAAI,CAAC,CAAA;oBACR,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;oBAC/C,GAAG,IAAI,CAAC,CAAA;oBACR,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC,CAAA;oBACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CACnB,IAAA,4BAAS,EAAC,KAAK,EAAE,GAAG,CAAC,EACrB,IAAA,4BAAS,EAAC,KAAK,EAAE,GAAG,GAAG,CAAC,CAAC,EACzB,GAAG,CACJ,CAAA;wBACD,GAAG,IAAI,EAAE,CAAA;oBACX,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YACD,IAAA,wBAAc,EAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;YAC9C,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QACtC,CAAC;QAED,OAAO;YACL,GAAG,GAAG;YACN,GAAG,EAAE,IAAI;YACT,QAAQ;YACR,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,aAAa;YACb,UAAU;YACV,OAAO,EAAE,IAAA,wBAAc,EAAC,UAAU,CAAC;YACnC,QAAQ;YACR,KAAK;YACL,YAAY;YACZ,YAAY;SACb,CAAA;IACH,CAAC;IAED;;;;;;OAMG;IACO,YAAY,CACpB,GAAa,EACb,GAAW,EACX,EAAE,QAAQ,EAAE,KAAK,EAAa;QAE9B,MAAM,EAAE,QAAQ,EAAE,GAAG,GAAG,CAAA;QACxB,IAAI,KAAgC,CAAA;QACpC,IAAI,QAAQ,EAAE,CAAC;YACb,0DAA0D;YAC1D,IAAI,GAAG,GACL,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YACrE,OAAO,KAAK,KAAK,SAAS,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACtC,KAAK,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;gBACrB,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;oBACxB,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;oBACxC,MAAM,UAAU,GAAG,MAAM,GAAG,CAAC,GAAG,CAAC,CAAA;oBACjC,GAAG,GAAG,GAAG,GAAG,UAAU,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;gBAC3C,CAAC;YACH,CAAC;YACD,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAA;QACvB,CAAC;QACD,OAAO,KAAK,CAAA;IACd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package/dist/indexFile.d.ts

@@ -33,13 +33,19 @@ export interface IndexData {
     indices: (refId: number) => RefIndex | undefined;
     maxRefLength: number;
     skipLines?: number;
-    maxBinNumber?: number;
     maxBlockSize: number;
     firstDataLine?: VirtualOffset;
     refCount?: number;
     csi?: boolean;
     csiVersion?: number;
-    depth?: number;
+    /**
+     * The binning scheme. TBI reports these too, though its own are fixed by the
+     * format (minShift 14, depth 5) rather than read from the file: they are the
+     * same scheme, and CSI exists to let a file choose other values for them.
+     */
+    minShift: number;
+    depth: number;
+    maxBinNumber: number;
 }
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
@@ -48,6 +54,25 @@ export default abstract class IndexFile {
         filehandle: GenericFilehandle;
     });
     protected abstract _parse(opts: Options): Promise<IndexData>;
+    /**
+     * The bins that may overlap [beg, end), as one inclusive [first, last] range
+     * per level of the binning scheme.
+     */
+    protected abstract reg2bins(beg: number, end: number, indexData: IndexData): (readonly [number, number])[];
+    /**
+     * The earliest virtual offset any record overlapping `beg` can have, so that
+     * chunks ending at or before it can be dropped. TBI reads it off the linear
+     * index; CSI, which has none, off the bins' loffsets.
+     */
+    protected abstract lowestOffset(ref: RefIndex, beg: number, indexData: IndexData): VirtualOffset | undefined;
+    /**
+     * The whole index file, decompressed, with a DataView over it. Both .tbi and
+     * .csi are bgzf-compressed and read whole, so both parsers start here.
+     */
+    protected readIndexBytes(opts: Options): Promise<{
+        bytes: Uint8Array<ArrayBufferLike>;
+        dataView: DataView<ArrayBufferLike>;
+    }>;
     /** @internal */
     lineCount(refName: string, opts?: Options): Promise<number>;
     /** @internal */
@@ -64,16 +89,28 @@ export default abstract class IndexFile {
         format: string;
         maxRefLength: number;
         skipLines?: number;
-        maxBinNumber?: number;
         maxBlockSize: number;
         firstDataLine?: VirtualOffset;
         refCount?: number;
         csi?: boolean;
         csiVersion?: number;
-        depth?: number;
+        /**
+         * The binning scheme. TBI reports these too, though its own are fixed by the
+         * format (minShift 14, depth 5) rather than read from the file: they are the
+         * same scheme, and CSI exists to let a file choose other values for them.
+         */
+        minShift: number;
+        depth: number;
+        maxBinNumber: number;
     }>;
-    /** @internal */
-    abstract blocksForRange(refName: string, start: number, end: number, opts: Options): Promise<Chunk[]>;
+    /**
+     * The chunks of the data file that may hold records overlapping the region.
+     * The two index formats differ only in their binning scheme and in where
+     * they keep the pruning floor, which is what the two hooks above supply.
+     *
+     * @internal
+     */
+    blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
     /** @internal */
     parse(opts?: Options): Promise<IndexData>;
     /** @internal */

package/dist/indexFile.js

@@ -1,11 +1,28 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const util_ts_1 = require("./util.js");
 class IndexFile {
     filehandle;
     parseP;
     constructor({ filehandle }) {
         this.filehandle = filehandle;
     }
+    /**
+     * The whole index file, decompressed, with a DataView over it. Both .tbi and
+     * .csi are bgzf-compressed and read whole, so both parsers start here.
+     */
+    async readIndexBytes(opts) {
+        const buf = await this.filehandle.readFile({
+            signal: opts.signal,
+            onProgress: opts.onProgress,
+        });
+        const bytes = await (0, bgzf_filehandle_1.unzip)(buf);
+        return {
+            bytes,
+            dataView: new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength),
+        };
+    }
     /** @internal */
     async lineCount(refName, opts = {}) {
         const indexData = await this.parse(opts);
@@ -20,6 +37,37 @@ class IndexFile {
         const { indices: _indices, ...rest } = await this.parse(opts);
         return rest;
     }
+    /**
+     * The chunks of the data file that may hold records overlapping the region.
+     * The two index formats differ only in their binning scheme and in where
+     * they keep the pruning floor, which is what the two hooks above supply.
+     *
+     * @internal
+     */
+    async blocksForRange(refName, min, max, opts = {}) {
+        const indexData = await this.parse(opts);
+        const refId = indexData.refNameToId[refName];
+        if (refId === undefined) {
+            return [];
+        }
+        const ba = indexData.indices(refId);
+        if (!ba) {
+            return [];
+        }
+        // Find chunks in overlapping bins. Leaf bins are not pruned.
+        const chunks = [];
+        for (const [start, end] of this.reg2bins(min, max, indexData)) {
+            for (let bin = start; bin <= end; bin++) {
+                const binChunks = ba.binIndex[bin];
+                if (binChunks) {
+                    for (const c of binChunks) {
+                        chunks.push(c);
+                    }
+                }
+            }
+        }
+        return (0, util_ts_1.optimizeChunks)(chunks, this.lowestOffset(ba, min, indexData));
+    }
     /** @internal */
     async parse(opts = {}) {
         this.parseP ??= this._parse(opts).catch((error) => {

package/dist/indexFile.js.map

@@ -1 +1 @@
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