@gmod/tabix 3.5.2 → 3.5.4

package/dist/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;
@@ -65,24 +67,73 @@ 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
+     * file whose header row is not commented keeps it. Empty when the index
+     * records no skipped lines.
+     *
+     * Deliberately not part of `getHeader`. htslib draws the same distinction:
+     * its indexer treats a line as non-data when `lineno <= line_skip` OR it
+     * begins with the meta character (tbx.c), while `tabix -H` prints only the
+     * leading meta-character lines and never consults line_skip (tabix.c).
+     * `getHeader` mirrors `-H`, so a bare header row is absent from it, and
+     * callers that need one were left re-reading the file themselves — guessing
+     * at a read size, and unable to tell a headerless file from an uncommented
+     * one. PLINK `.ld`, bedGraph and BED deflines are all routinely written this
+     * way.
+     */
+    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/dist/tabixIndexedFile.js

@@ -184,6 +184,46 @@ 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++) {
@@ -204,6 +244,7 @@ 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({
@@ -403,33 +444,95 @@ 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 (0, bgzf_filehandle_1.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 (0, bgzf_filehandle_1.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
+     * file whose header row is not commented keeps it. Empty when the index
+     * records no skipped lines.
+     *
+     * Deliberately not part of `getHeader`. htslib draws the same distinction:
+     * its indexer treats a line as non-data when `lineno <= line_skip` OR it
+     * begins with the meta character (tbx.c), while `tabix -H` prints only the
+     * leading meta-character lines and never consults line_skip (tabix.c).
+     * `getHeader` mirrors `-H`, so a bare header row is absent from it, and
+     * callers that need one were left re-reading the file themselves — guessing
+     * at a read size, and unable to tell a headerless file from an uncommented
+     * one. PLINK `.ld`, bedGraph and BED deflines are all routinely written this
+     * way.
+     */
+    async getSkippedLines(opts = {}) {
+        const { skipLines = 0 } = await this.getMetadata(opts);
+        // the index already answers this without reading the file at all
+        if (skipLines <= 0) {
+            return [];
         }
-        return bytes;
+        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);

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package/dist/tbi.d.ts

@@ -1,12 +1,25 @@
-import Chunk from './chunk.ts';
 import IndexFile from './indexFile.ts';
 import type { Options, RefIndex } from './indexFile.ts';
 import type VirtualOffset from './virtualOffset.ts';
 export default class TabixIndex extends IndexFile {
+    /**
+     * The bins that may overlap [beg, end) (zero-based half-open). TBI's scheme
+     * is CSI's with minShift/depth fixed, so this is CSI's reg2bins with the
+     * levels unrolled and its float shifts replaced by int32 ones.
+     */
+    protected reg2bins(beg: number, end: number): (readonly [number, number])[];
+    /**
+     * The linear index is monotonically non-decreasing, so the minimum virtual
+     * offset for chunks that could overlap [beg, ...) is its entry for beg.
+     * SYNC: ~/src/gmod/bam-js/src/bai.ts getLowestChunk
+     */
+    protected lowestOffset(ref: RefIndex, beg: number): VirtualOffset | undefined;
     /** @internal */
     _parse(opts?: Options): Promise<{
         indices: (refId: number) => RefIndex | undefined;
         metaChar: string | undefined;
+        minShift: number;
+        depth: number;
         maxBinNumber: number;
         maxRefLength: number;
         skipLines: number;
@@ -22,5 +35,4 @@ export default class TabixIndex extends IndexFile {
         refNameToId: Record<string, number>;
         maxBlockSize: number;
     }>;
-    blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
 }

package/dist/tbi.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");
@@ -11,31 +10,44 @@ const virtualOffset_ts_1 = require("./virtualOffset.js");
 const TBI_MAGIC = 21_578_324; // TBI\1
 // TBI is always the fixed depth-5, 14-bit-leaf binning scheme
 const TBI_DEPTH = 5;
-const TBI_MAX_REF_LENGTH = 2 ** (14 + TBI_DEPTH * 3);
-/**
- * calculate the list of bins that may overlap with region [beg,end)
- * (zero-based half-open)
- */
-function reg2bins(beg, end) {
-    // Clamp into the binning scheme's range. Past 2**31 the shifts below
-    // truncate to int32 and go negative, which would silently yield no bins.
-    const b = Math.min(Math.max(beg, 0), TBI_MAX_REF_LENGTH);
-    const e = Math.min(end, TBI_MAX_REF_LENGTH) - 1;
-    const bins = [];
-    if (b <= e) {
-        bins.push([0, 0], [1 + (b >> 26), 1 + (e >> 26)], [9 + (b >> 23), 9 + (e >> 23)], [73 + (b >> 20), 73 + (e >> 20)], [585 + (b >> 17), 585 + (e >> 17)], [4681 + (b >> 14), 4681 + (e >> 14)]);
-    }
-    return bins;
+const TBI_MIN_SHIFT = 14;
+const TBI_MAX_REF_LENGTH = 2 ** (TBI_MIN_SHIFT + TBI_DEPTH * 3);
+// Clamp a query coordinate into the binning scheme's range. Past 2**31 the
+// int32 shifts below truncate and go negative, which would silently yield no
+// bins.
+function clampToRefLength(pos) {
+    return Math.min(Math.max(pos, 0), TBI_MAX_REF_LENGTH);
 }
 class TabixIndex extends indexFile_ts_1.default {
+    /**
+     * The bins that may overlap [beg, end) (zero-based half-open). TBI's scheme
+     * is CSI's with minShift/depth fixed, so this is CSI's reg2bins with the
+     * levels unrolled and its float shifts replaced by int32 ones.
+     */
+    reg2bins(beg, end) {
+        if (beg > TBI_MAX_REF_LENGTH) {
+            console.warn('querying outside of possible tabix range');
+        }
+        const b = clampToRefLength(beg);
+        const e = Math.min(end, TBI_MAX_REF_LENGTH) - 1;
+        const bins = [];
+        if (b <= e) {
+            bins.push([0, 0], [1 + (b >> 26), 1 + (e >> 26)], [9 + (b >> 23), 9 + (e >> 23)], [73 + (b >> 20), 73 + (e >> 20)], [585 + (b >> 17), 585 + (e >> 17)], [4681 + (b >> 14), 4681 + (e >> 14)]);
+        }
+        return bins;
+    }
+    /**
+     * The linear index is monotonically non-decreasing, so the minimum virtual
+     * offset for chunks that could overlap [beg, ...) is its entry for beg.
+     * SYNC: ~/src/gmod/bam-js/src/bai.ts getLowestChunk
+     */
+    lowestOffset(ref, beg) {
+        const linearIndex = ref.linearIndex;
+        return linearIndex?.[Math.min(clampToRefLength(beg) >> TBI_MIN_SHIFT, linearIndex.length - 1)];
+    }
     /** @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);
         if (dataView.getUint32(0, true) !== TBI_MAGIC) {
             throw new Error('Not a TBI file');
         }
@@ -124,6 +136,8 @@ class TabixIndex extends indexFile_ts_1.default {
         return {
             indices: (0, util_ts_1.memoizeByRefId)(getIndices),
             metaChar,
+            minShift: TBI_MIN_SHIFT,
+            depth: TBI_DEPTH,
             maxBinNumber,
             maxRefLength: TBI_MAX_REF_LENGTH,
             skipLines,
@@ -136,42 +150,6 @@ class TabixIndex extends indexFile_ts_1.default {
             maxBlockSize: 1 << 16,
         };
     }
-    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 [];
-        }
-        if (min > TBI_MAX_REF_LENGTH) {
-            console.warn('querying outside of possible tabix range');
-        }
-        // clamp before the >> 14 below, which would truncate to int32 and go
-        // negative past 2**31
-        const beg = Math.min(Math.max(min, 0), TBI_MAX_REF_LENGTH);
-        const overlappingBins = reg2bins(min, max); // List of bin #s that overlap 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);
-                    }
-                }
-            }
-        }
-        // The linear index is monotonically non-decreasing, so the minimum virtual
-        // offset for chunks that could overlap [min, ...) is at index minLin.
-        // SYNC: ~/src/gmod/bam-js/src/bai.ts getLowestChunk
-        const linearIndex = ba.linearIndex;
-        const lowest = linearIndex?.[Math.min(beg >> 14, linearIndex.length - 1)];
-        return (0, util_ts_1.optimizeChunks)(chunks, lowest);
-    }
 }
 exports.default = TabixIndex;
 //# sourceMappingURL=tbi.js.map

package/dist/tbi.js.map

@@ -1 +1 @@
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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])[];
 }