@gmod/bam 7.6.1 → 7.7.0

package/dist/bamFile.js

@@ -15,6 +15,11 @@ const sam_ts_1 = require("./sam.js");
 const util_ts_1 = require("./util.js");
 exports.BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
+// Ceiling on the header read. A million contigs is roughly 10MB of compressed
+// @SQ lines and ref-seq table, so anything past this is a corrupt header
+// claiming a huge n_ref rather than a real one, and growing the read further
+// just downloads the file.
+const maxHeaderReadLen = 32 * 1024 * 1024;
 function resolveFilehandle(filehandle, path, url) {
     return (filehandle ??
         (path ? new generic_filehandle2_1.LocalFile(path) : url ? new generic_filehandle2_1.RemoteFile(url) : undefined));
@@ -131,40 +136,60 @@ class BamFile {
     }
     async getHeaderPre(opts = {}) {
         if (!this.index) {
-            return undefined;
+            // Only reachable via `new BamFile({htsget: true})` used directly rather
+            // than through HtsgetFile, which overrides this. Throwing rather than
+            // returning undefined keeps `| undefined` off getHeader()'s public type,
+            // and makes that misuse loud instead of silently answering every query
+            // with zero records (getSeqId would find no chrToIndex).
+            throw new Error('no index to read a header from: use HtsgetFile for htsget sources');
         }
         const indexData = await this.index.parse(opts);
-        // firstDataLine is not defined in cases where there is no data in the file
-        // (just bam header and nothing else)
-        const readLen = indexData.firstDataLine === undefined
-            ? undefined
+        // The records start at firstDataLine, so reading up to it plus the bgzf
+        // block straddling it covers the header. It is undefined when the index
+        // records no data at all (header-only BAM), and it undershoots when the
+        // index leaves offsets unset, so grow the read until the ref-seq table
+        // parses. Never readFile() here: on a remote BAM that is a whole-file
+        // download to read a header.
+        let readLen = indexData.firstDataLine === undefined
+            ? blockLen
             : indexData.firstDataLine.blockPosition + blockLen;
-        const buffer = readLen === undefined
-            ? await this.bam.readFile()
-            : await this.bam.read(readLen, 0);
-        let uncba = await (0, bgzf_filehandle_1.unzip)(buffer);
+        let samHeader;
+        let atEof = false;
+        while (samHeader === undefined && !atEof && readLen <= maxHeaderReadLen) {
+            const buffer = await this.bam.read(readLen, 0, { signal: opts.signal });
+            // a short read means readLen ran past the end of the file, so there are
+            // no more bytes to grow into
+            atEof = buffer.length < readLen;
+            samHeader = this.applyHeader(await (0, bgzf_filehandle_1.unzip)(buffer));
+            readLen *= 2;
+        }
+        if (samHeader === undefined) {
+            throw new Error('Insufficient data for reference sequences');
+        }
+        return samHeader;
+    }
+    /**
+     * Installs the header text and ref name/id maps from the start of a
+     * decompressed BAM stream, returning the parsed SAM header lines. Returns
+     * undefined if the stream is cut off partway through the ref-seq table, so
+     * the caller can retry with more data.
+     */
+    applyHeader(uncba) {
         const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
         if (dataView.getInt32(0, true) !== exports.BAM_MAGIC) {
             throw new Error('Not a BAM file');
         }
         const headLen = dataView.getInt32(4, true);
-        this.header = new TextDecoder('utf8').decode(uncba.subarray(8, 8 + headLen));
-        // BAM files with many reference sequences may need more data than the
-        // initial read covers. If the first attempt comes up short, fall back to
-        // reading the whole file (the index's firstDataLine is just an
-        // optimization hint, not a guaranteed cap on the ref-seq table size).
-        const refSeqStart = headLen + 8;
-        let parsed = (0, util_ts_1.parseRefSeqs)(uncba, refSeqStart, this.renameRefSeq);
-        if (!parsed) {
-            uncba = await (0, bgzf_filehandle_1.unzip)(await this.bam.readFile());
-            parsed = (0, util_ts_1.parseRefSeqs)(uncba, refSeqStart, this.renameRefSeq);
-        }
-        if (!parsed) {
-            throw new Error('Insufficient data for reference sequences');
+        const parsed = (0, util_ts_1.parseRefSeqs)(uncba, headLen + 8, this.renameRefSeq);
+        let samHeader;
+        if (parsed) {
+            const headerText = new TextDecoder('utf8').decode(uncba.subarray(8, 8 + headLen));
+            this.header = headerText;
+            this.chrToIndex = parsed.chrToIndex;
+            this.indexToChr = parsed.indexToChr;
+            samHeader = (0, sam_ts_1.parseHeaderText)(headerText);
         }
-        this.chrToIndex = parsed.chrToIndex;
-        this.indexToChr = parsed.indexToChr;
-        return (0, sam_ts_1.parseHeaderText)(this.header);
+        return samHeader;
     }
     getHeader(opts) {
         if (!this.headerP) {
@@ -347,21 +372,38 @@ class BamFile {
             const chunks = res[i];
             for (let j = 0, jl = chunks.length; j < jl; j++) {
                 const m = chunks[j];
-                map.set(m.toString(), m);
+                // Key on the virtual-offset span — the same key _cachedChunkFeatures
+                // uses. Chunk.toString() also folds in `bin` and fetchedSize(), which
+                // keeps two chunks covering an identical span apart here even though
+                // the cache below collapses them, so their records came back twice.
+                map.set(chunkCacheKey(m), m);
             }
         }
-        const mateFeatLists = await Promise.all([...map.values()].map(async (c) => {
-            const features = await this._cachedChunkFeatures(c, opts);
-            const mateRecs = [];
-            for (let i = 0, l = features.length; i < l; i++) {
-                const feature = features[i];
-                if (readNameCounts.get(feature.name) === 1 &&
-                    !readIds.has(feature.fileOffset)) {
-                    mateRecs.push(feature);
+        const mateChunks = [...map.values()];
+        // Bounded for the reason ADR 0008 bounds the main query path: a viewAsPairs
+        // query over a busy region resolves to many distinct mate chunks, and an
+        // unbounded fan-out inflates every one of them at once. Same inline pool
+        // shape as _fetchChunkFeatures — ADR 0009 measured extracting a shared
+        // mapConcurrent helper at ~11% on the hot path, so it stays inline.
+        const mateFeatLists = new Array(mateChunks.length);
+        let next = 0;
+        const readNext = async () => {
+            while (next < mateChunks.length) {
+                const ci = next++;
+                const features = await this._cachedChunkFeatures(mateChunks[ci], opts);
+                const mateRecs = [];
+                for (let i = 0, l = features.length; i < l; i++) {
+                    const feature = features[i];
+                    if (readNameCounts.get(feature.name) === 1 &&
+                        !readIds.has(feature.fileOffset)) {
+                        mateRecs.push(feature);
+                    }
                 }
+                mateFeatLists[ci] = mateRecs;
             }
-            return mateRecs;
-        }));
+        };
+        const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, mateChunks.length);
+        await Promise.all(Array.from({ length: workers }, () => readNext()));
         return mateFeatLists.flat();
     }
     async _readChunkFeatures(chunk, opts) {
@@ -379,6 +421,11 @@ class BamFile {
             bytes: data.byteLength,
         };
     }
+    // cpositions/dpositions are `ArrayLike`, not `number[]`, because the wasm
+    // decompressor produces them as Float64Arrays — @gmod/bgzf-filehandle spreads
+    // them into plain arrays on the way out, and this signature is what lets that
+    // copy be dropped there without a change here. Only indexed reads and
+    // `.length` are used below either way.
     readBamFeatures(ba, cpositions, dpositions, chunk) {
         let blockStart = 0;
         const sink = [];

package/dist/bamFile.js.map

@@ -1 +1 @@
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package/dist/chunk.d.ts

@@ -6,6 +6,5 @@ export default class Chunk {
     endPosition: number;
     constructor(minv: Offset, maxv: Offset, bin: number, endPosition?: number);
     toString(): string;
-    compareTo(b: Chunk): number;
     fetchedSize(): number;
 }

package/dist/chunk.js

@@ -19,11 +19,6 @@ class Chunk {
     toString() {
         return `${this.minv.toString()}..${this.maxv.toString()} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
     }
-    compareTo(b) {
-        return (this.minv.compareTo(b.minv) ||
-            this.maxv.compareTo(b.maxv) ||
-            this.bin - b.bin);
-    }
     fetchedSize() {
         return this.endPosition - this.minv.blockPosition;
     }

package/dist/chunk.js.map

@@ -1 +1 @@
-{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IACjB,IAAI,CAAQ;IACZ,IAAI,CAAQ;IACZ,GAAG,CAAQ;IAClB,2EAA2E;IAC3E,0EAA0E;IAC1E,8EAA8E;IAC9E,oEAAoE;IAC7D,WAAW,CAAQ;IAE1B,YACE,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,WAAW,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;QAE5C,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACnD,CAAC;CACF;AAvCD,wBAuCC"}
+{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IACjB,IAAI,CAAQ;IACZ,IAAI,CAAQ;IACZ,GAAG,CAAQ;IAClB,2EAA2E;IAC3E,0EAA0E;IAC1E,8EAA8E;IAC9E,oEAAoE;IAC7D,WAAW,CAAQ;IAE1B,YACE,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,WAAW,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;QAE5C,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACnD,CAAC;CACF;AA/BD,wBA+BC"}

package/dist/csi.d.ts

@@ -36,7 +36,6 @@ export default class CSI extends IndexFile {
         skipLines?: number | undefined;
         format?: string | undefined;
         formatFlags?: number | undefined;
-        csiVersion: number;
         firstDataLine: VirtualOffset | undefined;
         indices: (refId: number) => {
             binIndex: Record<number, Chunk[]>;
@@ -46,7 +45,6 @@ export default class CSI extends IndexFile {
         } | undefined;
         refCount: number;
         csi: boolean;
-        maxBlockSize: number;
     }>;
     protected getLowestChunk(): VirtualOffset;
     /**

package/dist/csi.js

@@ -92,17 +92,12 @@ class CSI extends indexFile_ts_1.default {
         const buffer = await this.filehandle.readFile(opts);
         const bytes = await (0, bgzf_filehandle_1.unzip)(buffer);
         const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
-        let csiVersion;
+        // CSI\1 and CSI\2 are parsed identically here — v2 only adds fields this
+        // reader doesn't consume — so the version is validated, not retained.
         const magic = dataView.getUint32(0, true);
-        if (magic === CSI1_MAGIC) {
-            csiVersion = 1;
-        }
-        else if (magic === CSI2_MAGIC) {
-            csiVersion = 2;
-        }
-        else {
-            throw new Error(`Not a CSI file ${magic}`);
+        if (magic !== CSI1_MAGIC && magic !== CSI2_MAGIC) {
             // TODO: do we need to support big-endian CSI files?
+            throw new Error(`Not a CSI file ${magic}`);
         }
         this.minShift = dataView.getInt32(4, true);
         this.depth = dataView.getInt32(8, true);
@@ -177,12 +172,10 @@ class CSI extends indexFile_ts_1.default {
             };
         }
         return {
-            csiVersion,
             firstDataLine,
             indices: (0, indexFile_ts_1.memoizeByRefId)(getIndices),
             refCount,
             csi: true,
-            maxBlockSize: 1 << 16,
             ...aux,
         };
     }

package/dist/csi.js.map

@@ -1 +1 @@
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package/dist/htsget.d.ts

@@ -2,14 +2,30 @@ import BamFile from './bamFile.ts';
 import type { BamRecordClass, BamRecordLike } from './bamFile.ts';
 import type BamRecord from './record.ts';
 import type { BamOpts, BaseOpts } from './util.ts';
+import type { Fetcher } from 'generic-filehandle2';
 export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends BamFile<T> {
     private baseUrl;
     private trackId;
+    private fetchFn;
     constructor(args: {
         trackId: string;
         baseUrl: string;
         recordClass?: BamRecordClass<T>;
+        /**
+         * fetch implementation used for every request, so an `Authorization: Bearer
+         * <token>` header can be added for servers that require one. It is also
+         * called with the data-block urls from the ticket, which may point at
+         * third-party hosts, so only attach credentials to hosts you trust — the
+         * spec has servers put whatever a data block needs in that url's own
+         * `headers` field, which is applied either way.
+         */
+        fetch?: Fetcher;
     });
+    /**
+     * Requests a ticket and returns its data blocks decompressed and
+     * concatenated, which per the spec is a complete BAM stream.
+     */
+    private fetchTicket;
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
     getHeaderPre(opts?: BaseOpts): Promise<{
         tag: string;

package/dist/htsget.js

@@ -39,91 +39,111 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const bamFile_ts_1 = __importStar(require("./bamFile.js"));
 const chunk_ts_1 = __importDefault(require("./chunk.js"));
-const sam_ts_1 = require("./sam.js");
 const util_ts_1 = require("./util.js");
 const virtualOffset_ts_1 = require("./virtualOffset.js");
-async function fetchOk(url, opts) {
-    const res = await fetch(url, opts);
+// Errors carry a JSON body naming the error type, e.g. {"htsget":
+// {"error":"InvalidAuthentication","message":"..."}}. Surface that rather than
+// the raw payload, since 401/403 are the first thing a misconfigured token hits.
+function htsgetErrorMessage(text) {
+    let parsed;
+    try {
+        parsed = JSON.parse(text);
+    }
+    catch {
+        // not JSON, fall through to the raw body
+    }
+    const err = parsed?.htsget;
+    return err?.error === undefined
+        ? text
+        : err.message === undefined
+            ? err.error
+            : `${err.error}: ${err.message}`;
+}
+/**
+ * Offset of the first alignment record in the concatenated ticket blocks.
+ *
+ * The spec has the client concatenate the blocks in ticket order to get a
+ * complete data stream, so whether the header is its own block is up to the
+ * server: htsnexus splits it into a leading `data:` url, while htsget-rs
+ * returns header and records together in a single url. Either way the
+ * concatenation starts with the BAM header, so seek past it rather than
+ * dropping blocks — a url count or class attribute can't tell the two layouts
+ * apart. Returns 0 when the stream has no header, which is what a server
+ * sending body-only blocks produces.
+ */
+function recordsOffset(uncba) {
+    const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
+    if (uncba.byteLength < 8 || dataView.getInt32(0, true) !== bamFile_ts_1.BAM_MAGIC) {
+        return 0;
+    }
+    const refs = (0, util_ts_1.parseRefSeqs)(uncba, 8 + dataView.getInt32(4, true), n => n);
+    if (!refs) {
+        throw new Error('truncated BAM header in htsget response');
+    }
+    return refs.end;
+}
+async function fetchOk(fetchFn, url, opts) {
+    const res = await fetchFn(url, opts);
     if (!res.ok) {
-        throw new Error(`HTTP ${res.status} fetching ${url}: ${await res.text()}`);
+        throw new Error(`HTTP ${res.status} fetching ${url}: ${htsgetErrorMessage(await res.text())}`);
     }
     return res;
 }
-async function fetchChunk({ url, headers }, opts) {
+async function fetchChunk(fetchFn, { url, headers }, opts) {
     // pass base64 data URLs straight to fetch; otherwise apply headers (minus
     // referer, which isn't a permitted client-set header).
     // https://stackoverflow.com/a/54123275/2129219
     const { referer: _referer, ...rest } = headers ?? {};
     const res = url.startsWith('data:')
-        ? await fetchOk(url)
-        : await fetchOk(url, { ...opts, headers: rest });
+        ? await fetchOk(fetchFn, url)
+        : await fetchOk(fetchFn, url, { ...opts, headers: rest });
     return new Uint8Array(await res.arrayBuffer());
 }
-async function fetchAndConcat(arr, opts) {
+async function fetchAndConcat(fetchFn, arr, opts) {
     // Pipeline unzip after each fetch so decompression overlaps later fetches.
-    return (0, util_ts_1.concatUint8Array)(await Promise.all(arr.map(async (c) => (0, bgzf_filehandle_1.unzip)(await fetchChunk(c, opts)))));
+    return (0, util_ts_1.concatUint8Array)(await Promise.all(arr.map(async (c) => (0, bgzf_filehandle_1.unzip)(await fetchChunk(fetchFn, c, opts)))));
 }
 class HtsgetFile extends bamFile_ts_1.default {
     baseUrl;
     trackId;
+    fetchFn;
     constructor(args) {
         super({ htsget: true, recordClass: args.recordClass });
         this.baseUrl = args.baseUrl;
         this.trackId = args.trackId;
+        this.fetchFn = args.fetch ?? ((input, init) => fetch(input, init));
+    }
+    /**
+     * Requests a ticket and returns its data blocks decompressed and
+     * concatenated, which per the spec is a complete BAM stream.
+     */
+    async fetchTicket(query, opts) {
+        const url = `${this.baseUrl}/${this.trackId}?${query}`;
+        const res = await fetchOk(this.fetchFn, url, { signal: opts?.signal });
+        const ticket = await res.json();
+        return fetchAndConcat(this.fetchFn, ticket.htsget.urls, {
+            signal: opts?.signal,
+        });
     }
     async getRecordsForRange(chr, min, max, opts) {
         await this.getHeader(opts);
-        const base = `${this.baseUrl}/${this.trackId}`;
-        const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
         const chrId = this.chrToIndex?.[chr];
         if (chrId === undefined) {
             return [];
         }
-        const result = await fetchOk(url, opts);
-        const data = await result.json();
-        const uncba = await fetchAndConcat(data.htsget.urls.slice(1), {
-            signal: opts?.signal,
-        });
+        const uncba = await this.fetchTicket(`referenceName=${chr}&start=${min}&end=${max}&format=BAM`, opts);
         const zero = new virtualOffset_ts_1.VirtualOffset(0, 0);
-        const allRecords = this.readBamFeatures(uncba, [], [], new chunk_ts_1.default(zero, zero, 0));
-        return (0, util_ts_1.appendInRange)(allRecords, chrId, min, max);
+        const records = this.readBamFeatures(uncba.subarray(recordsOffset(uncba)), [], [], new chunk_ts_1.default(zero, zero, 0));
+        return (0, util_ts_1.appendInRange)(records, chrId, min, max);
     }
     async getHeaderPre(opts = {}) {
-        const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
-        const result = await fetchOk(url, opts);
-        const data = await result.json();
-        const uncba = await fetchAndConcat(data.htsget.urls, {
-            signal: opts.signal,
-        });
-        const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
-        if (dataView.getInt32(0, true) !== bamFile_ts_1.BAM_MAGIC) {
-            throw new Error('Not a BAM file');
-        }
-        const headLen = dataView.getInt32(4, true);
-        const decoder = new TextDecoder();
-        const headerText = decoder.decode(uncba.subarray(8, 8 + headLen));
-        const samHeader = (0, sam_ts_1.parseHeaderText)(headerText);
-        // use the @SQ lines in the header to figure out the
-        // mapping between ref ref ID numbers and names
-        const idToName = [];
-        const nameToId = {};
-        const sqLines = samHeader.filter(l => l.tag === 'SQ');
-        for (const [refId, sqLine] of sqLines.entries()) {
-            let refName = '';
-            let length = 0;
-            for (const item of sqLine.data) {
-                if (item.tag === 'SN') {
-                    refName = item.value;
-                }
-                else if (item.tag === 'LN') {
-                    length = +item.value;
-                }
-            }
-            nameToId[refName] = refId;
-            idToName[refId] = { refName, length };
+        // format is the only parameter the spec permits alongside class=header;
+        // servers SHOULD reject anything else with InvalidInput
+        const uncba = await this.fetchTicket('class=header&format=BAM', opts);
+        const samHeader = this.applyHeader(uncba);
+        if (!samHeader) {
+            throw new Error('Insufficient data for reference sequences');
         }
-        this.chrToIndex = nameToId;
-        this.indexToChr = idToName;
         return samHeader;
     }
 }

package/dist/htsget.js.map

@@ -1 +1 @@
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+{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,2DAAiD;AACjD,0DAA8B;AAC9B,uCAAyE;AACzE,yDAAkD;AAuBlD,kEAAkE;AAClE,+EAA+E;AAC/E,iFAAiF;AACjF,SAAS,kBAAkB,CAAC,IAAY;IACtC,IAAI,MAAmC,CAAA;IACvC,IAAI,CAAC;QACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IAAC,MAAM,CAAC;QACP,yCAAyC;IAC3C,CAAC;IACD,MAAM,GAAG,GAAG,MAAM,EAAE,MAAM,CAAA;IAC1B,OAAO,GAAG,EAAE,KAAK,KAAK,SAAS;QAC7B,CAAC,CAAC,IAAI;QACN,CAAC,CAAC,GAAG,CAAC,OAAO,KAAK,SAAS;YACzB,CAAC,CAAC,GAAG,CAAC,KAAK;YACX,CAAC,CAAC,GAAG,GAAG,CAAC,KAAK,KAAK,GAAG,CAAC,OAAO,EAAE,CAAA;AACtC,CAAC;AAED;;;;;;;;;;;GAWG;AACH,SAAS,aAAa,CAAC,KAAiB;IACtC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;IACD,IAAI,KAAK,CAAC,UAAU,GAAG,CAAC,IAAI,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,sBAAS,EAAE,CAAC;QACrE,OAAO,CAAC,CAAA;IACV,CAAC;IACD,MAAM,IAAI,GAAG,IAAA,sBAAY,EAAC,KAAK,EAAE,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IACxE,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,MAAM,IAAI,KAAK,CAAC,yCAAyC,CAAC,CAAA;IAC5D,CAAC;IACD,OAAO,IAAI,CAAC,GAAG,CAAA;AACjB,CAAC;AAED,KAAK,UAAU,OAAO,CAAC,OAAgB,EAAE,GAAW,EAAE,IAAkB;IACtE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACpC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,kBAAkB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC,EAAE,CAC9E,CAAA;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,KAAK,UAAU,UAAU,CACvB,OAAgB,EAChB,EAAE,GAAG,EAAE,OAAO,EAAe,EAC7B,IAAkB;IAElB,0EAA0E;IAC1E,uDAAuD;IACvD,+CAA+C;IAC/C,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,IAAI,EAAE,CAAA;IACpD,MAAM,GAAG,GAAG,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC;QACjC,CAAC,CAAC,MAAM,OAAO,CAAC,OAAO,EAAE,GAAG,CAAC;QAC7B,CAAC,CAAC,MAAM,OAAO,CAAC,OAAO,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAC3D,OAAO,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;AAChD,CAAC;AAED,KAAK,UAAU,cAAc,CAC3B,OAAgB,EAChB,GAAkB,EAClB,IAAkB;IAElB,2EAA2E;IAC3E,OAAO,IAAA,0BAAgB,EACrB,MAAM,OAAO,CAAC,GAAG,CACf,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,CAAC,EAAC,EAAE,CAAC,IAAA,uBAAK,EAAC,MAAM,UAAU,CAAC,OAAO,EAAE,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAC9D,CACF,CAAA;AACH,CAAC;AAED,MAAqB,UAEnB,SAAQ,oBAAU;IACV,OAAO,CAAQ;IAEf,OAAO,CAAQ;IAEf,OAAO,CAAS;IAExB,YAAY,IAaX;QACC,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,CAAC,WAAW,EAAE,CAAC,CAAA;QACtD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,KAAK,IAAI,CAAC,CAAC,KAAK,EAAE,IAAI,EAAE,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;IACpE,CAAC;IAED;;;OAGG;IACK,KAAK,CAAC,WAAW,CAAC,KAAa,EAAE,IAAe;QACtD,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,IAAI,KAAK,EAAE,CAAA;QACtD,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;QACtE,MAAM,MAAM,GAAiB,MAAM,GAAG,CAAC,IAAI,EAAE,CAAA;QAC7C,OAAO,cAAc,CAAC,IAAI,CAAC,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE;YACtD,MAAM,EAAE,IAAI,EAAE,MAAM;SACrB,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;QAEd,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,WAAW,CAClC,iBAAiB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,EACzD,IAAI,CACL,CAAA;QACD,MAAM,IAAI,GAAG,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACpC,MAAM,OAAO,GAAG,IAAI,CAAC,eAAe,CAClC,KAAK,CAAC,QAAQ,CAAC,aAAa,CAAC,KAAK,CAAC,CAAC,EACpC,EAAE,EACF,EAAE,EACF,IAAI,kBAAK,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CACzB,CAAA;QACD,OAAO,IAAA,uBAAa,EAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;IAChD,CAAC;IAED,KAAK,CAAC,YAAY,CAAC,OAAiB,EAAE;QACpC,wEAAwE;QACxE,wDAAwD;QACxD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,yBAAyB,EAAE,IAAI,CAAC,CAAA;QACrE,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;QACzC,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CAAC,2CAA2C,CAAC,CAAA;QAC9D,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;CACF;AA7ED,6BA6EC"}

package/dist/index.d.ts

@@ -5,3 +5,4 @@ export { default as BamRecord } from './record.ts';
 export { default as HtsgetFile } from './htsget.ts';
 export type { Bytes } from './record.ts';
 export type { BamRecordClass, BamRecordLike } from './bamFile.ts';
+export type { Fetcher } from 'generic-filehandle2';

package/dist/indexFile.d.ts

@@ -1,6 +1,6 @@
 import type Chunk from './chunk.ts';
 import type { BaseOpts } from './util.ts';
-import type { Offset, VirtualOffset } from './virtualOffset.ts';
+import type { OffsetCoords, VirtualOffset } from './virtualOffset.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export interface Region {
     refId: number;
@@ -16,7 +16,6 @@ export interface RefIndex {
 export interface ParsedIndexBase<R extends RefIndex = RefIndex> {
     firstDataLine: VirtualOffset | undefined;
     refCount: number;
-    maxBlockSize: number;
     indices: (refId: number) => R | undefined;
 }
 export declare function memoizeByRefId<T>(getIndices: (refId: number) => T | undefined, maxSize?: number): (refId: number) => T | undefined;
@@ -35,7 +34,7 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
         score: number;
     }[]>;
     protected abstract reg2bins(min: number, max: number): readonly (readonly [number, number])[];
-    protected abstract getLowestChunk(refIndex: RefIndex, min: number): Offset | undefined;
+    protected abstract getLowestChunk(refIndex: RefIndex, min: number): OffsetCoords | undefined;
     blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
     parse(opts?: BaseOpts): Promise<TParsed>;
     lineCount(refId: number, opts?: BaseOpts): Promise<number>;