@gmod/tabix 3.5.3 → 3.5.5

package/esm/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/esm/csi.js

@@ -1,7 +1,6 @@
-import { unzip } from '@gmod/bgzf-filehandle';
 import Chunk from "./chunk.js";
 import IndexFile from "./indexFile.js";
-import { clampChunkEnds, memoizeByRefId, minVirtualOffset, optimizeChunks, parseAuxData, parsePseudoBin, } from "./util.js";
+import { clampChunkEnds, memoizeByRefId, minVirtualOffset, parseAuxData, parsePseudoBin, } from "./util.js";
 import { fromBytes } from "./virtualOffset.js";
 const CSI1_MAGIC = 21_582_659; // CSI\1
 const CSI2_MAGIC = 38_359_875; // CSI\2
@@ -14,17 +13,9 @@ function rshift(num, bits) {
     return Math.floor(num / 2 ** bits);
 }
 export default class CSI extends IndexFile {
-    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 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) {
@@ -36,11 +27,10 @@ export default class CSI extends IndexFile {
         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
             ? parseAuxData(bytes, 16)
@@ -118,40 +108,12 @@ export default class CSI extends IndexFile {
             firstDataLine,
             csiVersion,
             indices: 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 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
@@ -159,11 +121,12 @@ 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
      */
-    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) {
@@ -176,22 +139,22 @@ export default class CSI extends IndexFile {
         }
         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]);
         }

package/esm/csi.js.map

@@ -1 +1 @@
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+{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EACL,cAAc,EACd,cAAc,EACd,gBAAgB,EAChB,YAAY,EACZ,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;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,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;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,YAAY,CAAC,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,gBAAgB,CAAC,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,cAAc,CAAC,KAAK,EAAE,GAAG,GAAG,EAAE,CAAC,CAAA;oBACvC,GAAG,IAAI,EAAE,GAAG,EAAE,CAAA;gBAChB,CAAC;qBAAM,CAAC;oBACN,QAAQ,CAAC,GAAG,CAAC,GAAG,SAAS,CAAC,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,KAAK,CACnB,SAAS,CAAC,KAAK,EAAE,GAAG,CAAC,EACrB,SAAS,CAAC,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,cAAc,CAAC,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,cAAc,CAAC,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,CAA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package/esm/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/esm/indexFile.js

@@ -1,9 +1,26 @@
+import { unzip } from '@gmod/bgzf-filehandle';
+import { optimizeChunks } from "./util.js";
 export default 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 unzip(buf);
+        return {
+            bytes,
+            dataView: new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength),
+        };
+    }
     /** @internal */
     async lineCount(refName, opts = {}) {
         const indexData = await this.parse(opts);
@@ -18,6 +35,37 @@ export default 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 optimizeChunks(chunks, this.lowestOffset(ba, min, indexData));
+    }
     /** @internal */
     async parse(opts = {}) {
         this.parseP ??= this._parse(opts).catch((error) => {

package/esm/indexFile.js.map

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

@@ -1,5 +1,6 @@
 import type Chunk from './chunk.ts';
 import type { Options } from './indexFile.ts';
+import type { ChunkSlice } from '@gmod/bgzf-filehandle';
 import type { GenericFilehandle } from 'generic-filehandle2';
 type GetLinesCallback = (line: string, fileOffset: number, start: number, end: number) => void;
 interface GetLinesOpts {
@@ -21,6 +22,7 @@ export default class TabixIndexedFile {
     private filehandle;
     private index;
     private chunkCache;
+    private headerP?;
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, }: {
         path?: string;
         filehandle?: GenericFilehandle;
@@ -65,14 +67,37 @@ export default class TabixIndexedFile {
         format: string;
         maxRefLength: number;
         skipLines?: number;
-        maxBinNumber?: number;
         maxBlockSize: number;
         firstDataLine?: import("./virtualOffset.ts").default;
         refCount?: number;
         csi?: boolean;
         csiVersion?: number;
-        depth?: number;
+        minShift: number;
+        depth: number;
+        maxBinNumber: number;
     }>;
+    /**
+     * The file's leading blocks, decompressed: everything from the start through
+     * the end of the block holding the first data line.
+     */
+    private readHeaderBytes;
+    /**
+     * Both header forms, from one read of the same bytes: the commented block
+     * `tabix -H` prints, and the rows `tabix -S N` counted.
+     *
+     * Memoized, because asking for one and then the other is the normal way to
+     * find a header whichever way the file keeps it (see `getHeaderLines`), and
+     * that used to fetch and decompress the file's leading blocks twice. Only
+     * the parsed results are retained — the decompressed bytes are dropped,
+     * which matters for a VCF header that can run to megabytes.
+     */
+    private parseHeader;
+    private getParsedHeader;
+    /**
+     * The bytes of the commented header. Deliberately not memoized, unlike the
+     * string form: this hands back the buffer, and holding one for the lifetime
+     * of the file is the caller's decision to make.
+     */
     getHeaderBuffer(opts?: Options): Promise<Uint8Array<ArrayBufferLike>>;
     /**
      * The leading lines the index says to skip — `tabix -S N` — which is where a
@@ -91,14 +116,24 @@ export default class TabixIndexedFile {
      */
     getSkippedLines(opts?: Options): Promise<string[]>;
     getHeader(opts?: Options): Promise<string>;
+    /**
+     * The file's header lines, however that file keeps them: the meta-character
+     * block when there is one, and otherwise the rows the index counted. Empty
+     * lines are dropped.
+     *
+     * The two halves answer different questions (see `getSkippedLines`), but
+     * "what are this file's header lines" is nearly always the question a caller
+     * actually has, and answering it from `getHeader` alone is wrong in a way
+     * that doesn't announce itself: a bare header row comes back as the empty
+     * string, indistinguishable from a file that has no header, so callers fall
+     * back to an assumed column layout and quietly mis-name columns. Deciding it
+     * here also means one read of the leading blocks instead of two.
+     */
+    getHeaderLines(opts?: Options): Promise<string[]>;
     getReferenceSequenceNames(opts?: Options): Promise<string[]>;
     /** @param refName reference sequence name */
     lineCount(refName: string, opts?: Options): Promise<number>;
     /** @internal */
-    readChunk(c: Chunk, opts?: Options): Promise<{
-        buffer: Uint8Array<ArrayBufferLike>;
-        cpositions: number[];
-        dpositions: number[];
-    }>;
+    readChunk(c: Chunk, opts?: Options): Promise<ChunkSlice>;
 }
 export {};

package/esm/tabixIndexedFile.js

@@ -179,6 +179,46 @@ function getVcfEnd(buffer, startCoordinate, refStart, refEnd, infoStart, infoEnd
     }
     return endCoordinate;
 }
+const textDecoder = new TextDecoder();
+/**
+ * The leading run of meta-character lines — what `tabix -H` prints. Everything
+ * from the first line that doesn't begin with the meta character is dropped.
+ */
+function trimToMetaLines(bytes, metaChar) {
+    let lastNewline = -1;
+    const metaByte = metaChar.charCodeAt(0);
+    for (let i = 0, l = bytes.length; i < l; i++) {
+        const byte = bytes[i];
+        if (i === lastNewline + 1 && byte !== metaByte) {
+            break;
+        }
+        if (byte === NEWLINE) {
+            lastNewline = i;
+        }
+    }
+    return bytes.subarray(0, lastNewline + 1);
+}
+/**
+ * The first `count` lines. Scans for the count-th newline and decodes only that
+ * far, rather than decoding and splitting the whole buffer to keep its first
+ * few lines — the buffer runs to the first data line, which for a file with a
+ * long commented preamble above its counted rows can be megabytes.
+ */
+function firstLines(bytes, count) {
+    let end = 0;
+    for (let i = 0; i < count; i++) {
+        const n = bytes.indexOf(NEWLINE, end);
+        if (n === -1) {
+            end = bytes.length;
+            break;
+        }
+        end = n + 1;
+    }
+    return textDecoder
+        .decode(bytes.subarray(0, end))
+        .split(/\r?\n/)
+        .slice(0, count);
+}
 function parseIntFromBytes(buffer, start, end) {
     let val = 0;
     for (let i = start; i < end; i++) {
@@ -199,6 +239,7 @@ export default class TabixIndexedFile {
     filehandle;
     index;
     chunkCache;
+    headerP;
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, }) {
         this.filehandle = resolveFilehandle(filehandle, path, url);
         this.index = resolveIndex({
@@ -398,29 +439,52 @@ export default class TabixIndexedFile {
     async getMetadata(opts = {}) {
         return this.index.getMetadata(opts);
     }
-    async getHeaderBuffer(opts = {}) {
-        const { firstDataLine, metaChar, maxBlockSize } = await this.getMetadata(opts);
+    /**
+     * The file's leading blocks, decompressed: everything from the start through
+     * the end of the block holding the first data line.
+     */
+    async readHeaderBytes(opts) {
+        const { firstDataLine, maxBlockSize } = await this.getMetadata(opts);
         const maxFetch = (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
         const buf = await this.filehandle.read(maxFetch, 0, opts);
-        const bytes = (await unzip(buf));
-        // trim off lines after the last meta line
-        if (metaChar) {
-            let lastNewline = -1;
-            const metaByte = metaChar.charCodeAt(0);
-            for (let i = 0, l = bytes.length; i < l; i++) {
-                const byte = bytes[i];
-                if (i === lastNewline + 1 && byte !== metaByte) {
-                    break;
-                }
-                if (byte === NEWLINE) {
-                    lastNewline = i;
-                }
-            }
-            return bytes.subarray(0, lastNewline + 1);
-        }
-        return bytes;
+        return unzip(buf);
+    }
+    /**
+     * Both header forms, from one read of the same bytes: the commented block
+     * `tabix -H` prints, and the rows `tabix -S N` counted.
+     *
+     * Memoized, because asking for one and then the other is the normal way to
+     * find a header whichever way the file keeps it (see `getHeaderLines`), and
+     * that used to fetch and decompress the file's leading blocks twice. Only
+     * the parsed results are retained — the decompressed bytes are dropped,
+     * which matters for a VCF header that can run to megabytes.
+     */
+    async parseHeader(opts) {
+        const { metaChar, skipLines = 0 } = await this.getMetadata(opts);
+        const bytes = await this.readHeaderBytes(opts);
+        return {
+            header: textDecoder.decode(metaChar ? trimToMetaLines(bytes, metaChar) : bytes),
+            skippedLines: skipLines > 0 ? firstLines(bytes, skipLines) : [],
+        };
+    }
+    async getParsedHeader(opts = {}) {
+        this.headerP ??= this.parseHeader(opts).catch((error) => {
+            this.headerP = undefined;
+            throw error;
+        });
+        return this.headerP;
+    }
+    /**
+     * The bytes of the commented header. Deliberately not memoized, unlike the
+     * string form: this hands back the buffer, and holding one for the lifetime
+     * of the file is the caller's decision to make.
+     */
+    async getHeaderBuffer(opts = {}) {
+        const { metaChar } = await this.getMetadata(opts);
+        const bytes = await this.readHeaderBytes(opts);
+        return metaChar ? trimToMetaLines(bytes, metaChar) : bytes;
     }
     /**
      * The leading lines the index says to skip — `tabix -S N` — which is where a
@@ -438,19 +502,32 @@ export default class TabixIndexedFile {
      * way.
      */
     async getSkippedLines(opts = {}) {
-        const { firstDataLine, skipLines = 0, maxBlockSize, } = await this.getMetadata(opts);
+        const { skipLines = 0 } = await this.getMetadata(opts);
+        // the index already answers this without reading the file at all
         if (skipLines <= 0) {
             return [];
         }
-        // same read getHeaderBuffer makes, and the same caveat: a header spanning
-        // more blocks than this is not covered
-        const buf = await this.filehandle.read((firstDataLine?.blockPosition ?? 0) + maxBlockSize, 0, opts);
-        const bytes = (await unzip(buf));
-        return new TextDecoder().decode(bytes).split(/\r?\n/).slice(0, skipLines);
+        return (await this.getParsedHeader(opts)).skippedLines;
     }
     async getHeader(opts = {}) {
-        const bytes = await this.getHeaderBuffer(opts);
-        return new TextDecoder().decode(bytes);
+        return (await this.getParsedHeader(opts)).header;
+    }
+    /**
+     * The file's header lines, however that file keeps them: the meta-character
+     * block when there is one, and otherwise the rows the index counted. Empty
+     * lines are dropped.
+     *
+     * The two halves answer different questions (see `getSkippedLines`), but
+     * "what are this file's header lines" is nearly always the question a caller
+     * actually has, and answering it from `getHeader` alone is wrong in a way
+     * that doesn't announce itself: a bare header row comes back as the empty
+     * string, indistinguishable from a file that has no header, so callers fall
+     * back to an assumed column layout and quietly mis-name columns. Deciding it
+     * here also means one read of the leading blocks instead of two.
+     */
+    async getHeaderLines(opts = {}) {
+        const { header, skippedLines } = await this.getParsedHeader(opts);
+        return (header ? header.split(/\r?\n/) : skippedLines).filter(Boolean);
     }
     async getReferenceSequenceNames(opts = {}) {
         const metadata = await this.getMetadata(opts);