@gmod/bam 1.1.18 → 2.0.0

package/esm/bamFile.js

@@ -1,49 +1,52 @@
+import { Buffer } from 'buffer';
 import crc32 from 'buffer-crc32';
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
-import entries from 'object.entries-ponyfill';
 import { LocalFile, RemoteFile } from 'generic-filehandle';
 import AbortablePromiseCache from 'abortable-promise-cache';
 import QuickLRU from 'quick-lru';
-//locals
+// locals
 import BAI from './bai';
 import CSI from './csi';
 import BAMFeature from './record';
 import { parseHeaderText } from './sam';
-import { abortBreakPoint, checkAbortSignal, timeout, makeOpts, } from './util';
+import { checkAbortSignal, timeout, makeOpts } from './util';
 export const BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
-function flat(arr) {
-    return [].concat(...arr);
-}
 async function gen2array(gen) {
-    const out = [];
+    let out = [];
     for await (const x of gen) {
-        out.push(x);
+        out = out.concat(x);
     }
     return out;
 }
+class NullFilehandle {
+    read() {
+        throw new Error('never called');
+    }
+    stat() {
+        throw new Error('never called');
+    }
+    readFile() {
+        throw new Error('never called');
+    }
+    close() {
+        throw new Error('never called');
+    }
+}
 export default class BamFile {
-    /**
-     * @param {object} args
-     * @param {string} [args.bamPath]
-     * @param {FileHandle} [args.bamFilehandle]
-     * @param {string} [args.baiPath]
-     * @param {FileHandle} [args.baiFilehandle]
-     */
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, fetchSizeLimit, chunkSizeLimit, yieldThreadTime = 100, renameRefSeqs = n => n, }) {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime = 100, renameRefSeqs = n => n, }) {
+        this.htsget = false;
         this.featureCache = new AbortablePromiseCache({
-            //@ts-ignore
             cache: new QuickLRU({
                 maxSize: 50,
             }),
-            //@ts-ignore
-            fill: async ({ chunk, opts }, signal) => {
+            fill: async (args, signal) => {
+                const { chunk, opts } = args;
                 const { data, cpositions, dpositions } = await this._readChunk({
                     chunk,
                     opts: { ...opts, signal },
                 });
-                const feats = await this.readBamFeatures(data, cpositions, dpositions, chunk);
-                return feats;
+                return this.readBamFeatures(data, cpositions, dpositions, chunk);
             },
         });
         this.renameRefSeq = renameRefSeqs;
@@ -56,6 +59,10 @@ export default class BamFile {
         else if (bamUrl) {
             this.bam = new RemoteFile(bamUrl);
         }
+        else if (htsget) {
+            this.htsget = true;
+            this.bam = new NullFilehandle();
+        }
         else {
             throw new Error('unable to initialize bam');
         }
@@ -83,33 +90,31 @@ export default class BamFile {
         else if (bamUrl) {
             this.index = new BAI({ filehandle: new RemoteFile(`${bamUrl}.bai`) });
         }
+        else if (htsget) {
+            this.htsget = true;
+        }
         else {
             throw new Error('unable to infer index format');
         }
-        this.fetchSizeLimit = fetchSizeLimit || 500000000; // 500MB
-        this.chunkSizeLimit = chunkSizeLimit || 300000000; // 300MB
         this.yieldThreadTime = yieldThreadTime;
     }
-    async getHeader(origOpts = {}) {
+    async getHeaderPre(origOpts) {
         const opts = makeOpts(origOpts);
+        if (!this.index) {
+            return;
+        }
         const indexData = await this.index.parse(opts);
         const ret = indexData.firstDataLine
             ? indexData.firstDataLine.blockPosition + 65535
             : undefined;
         let buffer;
         if (ret) {
-            const res = await this.bam.read(Buffer.alloc(ret + blockLen), 0, ret + blockLen, 0, opts);
-            const { bytesRead } = res;
-            ({ buffer } = res);
-            if (!bytesRead) {
+            const s = ret + blockLen;
+            const res = await this.bam.read(Buffer.alloc(s), 0, s, 0, opts);
+            if (!res.bytesRead) {
                 throw new Error('Error reading header');
             }
-            if (bytesRead < ret) {
-                buffer = buffer.subarray(0, bytesRead);
-            }
-            else {
-                buffer = buffer.subarray(0, ret);
-            }
+            buffer = res.buffer.subarray(0, Math.min(res.bytesRead, ret));
         }
         else {
             buffer = (await this.bam.readFile(opts));
@@ -125,13 +130,22 @@ export default class BamFile {
         this.indexToChr = indexToChr;
         return parseHeaderText(this.header);
     }
+    getHeader(opts) {
+        if (!this.headerP) {
+            this.headerP = this.getHeaderPre(opts).catch(e => {
+                this.headerP = undefined;
+                throw e;
+            });
+        }
+        return this.headerP;
+    }
     async getHeaderText(opts = {}) {
         await this.getHeader(opts);
         return this.header;
     }
     // the full length of the refseq block is not given in advance so this grabs
     // a chunk and doubles it if all refseqs haven't been processed
-    async _readRefSeqs(start, refSeqBytes, opts = {}) {
+    async _readRefSeqs(start, refSeqBytes, opts) {
         if (start > refSeqBytes) {
             return this._readRefSeqs(start, refSeqBytes * 2, opts);
         }
@@ -159,54 +173,29 @@ export default class BamFile {
         }
         return { chrToIndex, indexToChr };
     }
-    async getRecordsForRange(chr, min, max, opts = {
-        viewAsPairs: false,
-        pairAcrossChr: false,
-        maxInsertSize: 200000,
-    }) {
-        return flat(await gen2array(this.streamRecordsForRange(chr, min, max, opts)));
+    async getRecordsForRange(chr, min, max, opts) {
+        return gen2array(this.streamRecordsForRange(chr, min, max, opts));
     }
-    async *streamRecordsForRange(chr, min, max, opts = {}) {
-        const { signal } = opts;
-        const chrId = this.chrToIndex && this.chrToIndex[chr];
-        let chunks;
-        if (!(chrId >= 0)) {
-            chunks = [];
+    async *streamRecordsForRange(chr, min, max, opts) {
+        var _a;
+        await this.getHeader(opts);
+        const chrId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[chr];
+        if (chrId === undefined || !this.index) {
+            yield [];
         }
         else {
-            chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
-            if (!chunks) {
-                throw new Error('Error in index fetch');
-            }
-        }
-        for (let i = 0; i < chunks.length; i += 1) {
-            await abortBreakPoint(signal);
-            const size = chunks[i].fetchedSize();
-            if (size > this.chunkSizeLimit) {
-                throw new Error(`Too many BAM features. BAM chunk size ${size} bytes exceeds chunkSizeLimit of ${this.chunkSizeLimit}`);
-            }
+            const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
+            yield* this._fetchChunkFeatures(chunks, chrId, min, max, opts);
         }
-        const totalSize = chunks
-            .map(s => s.fetchedSize())
-            .reduce((a, b) => a + b, 0);
-        if (totalSize > this.fetchSizeLimit) {
-            throw new Error(`data size of ${totalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);
-        }
-        yield* this._fetchChunkFeatures(chunks, chrId, min, max, opts);
     }
-    async *_fetchChunkFeatures(chunks, chrId, min, max, opts) {
-        const { viewAsPairs = false } = opts;
+    async *_fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
+        const { viewAsPairs } = opts;
         const feats = [];
         let done = false;
-        for (let i = 0; i < chunks.length; i++) {
-            const c = chunks[i];
-            const records = (await this.featureCache.get(c.toString(), {
-                chunk: c,
-                opts,
-            }, opts.signal));
+        for (const chunk of chunks) {
+            const records = await this.featureCache.get(chunk.toString(), { chunk, opts }, opts.signal);
             const recs = [];
-            for (let i = 0; i < records.length; i += 1) {
-                const feature = records[i];
+            for (const feature of records) {
                 if (feature.seq_id() === chrId) {
                     if (feature.get('start') >= max) {
                         // past end of range, can stop iterating
@@ -231,35 +220,35 @@ export default class BamFile {
         }
     }
     async fetchPairs(chrId, feats, opts) {
-        const { pairAcrossChr = false, maxInsertSize = 200000 } = opts;
+        const { pairAcrossChr, maxInsertSize = 200000 } = opts;
         const unmatedPairs = {};
         const readIds = {};
         feats.map(ret => {
             const readNames = {};
-            for (let i = 0; i < ret.length; i++) {
-                const name = ret[i].name();
-                const id = ret[i].id();
+            for (const element of ret) {
+                const name = element.name();
+                const id = element.id();
                 if (!readNames[name]) {
                     readNames[name] = 0;
                 }
                 readNames[name]++;
                 readIds[id] = 1;
             }
-            entries(readNames).forEach(([k, v]) => {
+            for (const [k, v] of Object.entries(readNames)) {
                 if (v === 1) {
                     unmatedPairs[k] = true;
                 }
-            });
+            }
         });
         const matePromises = [];
         feats.map(ret => {
-            for (let i = 0; i < ret.length; i++) {
-                const f = ret[i];
+            for (const f of ret) {
                 const name = f.name();
                 const start = f.get('start');
                 const pnext = f._next_pos();
                 const rnext = f._next_refid();
-                if (unmatedPairs[name] &&
+                if (this.index &&
+                    unmatedPairs[name] &&
                     (pairAcrossChr ||
                         (rnext === chrId && Math.abs(start - pnext) < maxInsertSize))) {
                     matePromises.push(this.index.blocksForRange(rnext, pnext, pnext + 1, opts));
@@ -268,36 +257,35 @@ export default class BamFile {
         });
         // filter out duplicate chunks (the blocks are lists of chunks, blocks are
         // concatenated, then filter dup chunks)
-        const mateChunks = flat(await Promise.all(matePromises))
-            .sort()
-            .filter((item, pos, ary) => !pos || item.toString() !== ary[pos - 1].toString());
-        const mateTotalSize = mateChunks
-            .map(s => s.fetchedSize())
-            .reduce((a, b) => a + b, 0);
-        if (mateTotalSize > this.fetchSizeLimit) {
-            throw new Error(`data size of ${mateTotalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);
+        const map = new Map();
+        const res = await Promise.all(matePromises);
+        for (const m of res.flat()) {
+            if (!map.has(m.toString())) {
+                map.set(m.toString(), m);
+            }
         }
-        const mateFeatPromises = mateChunks.map(async (c) => {
+        const mateFeatPromises = await Promise.all([...map.values()].map(async (c) => {
             const { data, cpositions, dpositions, chunk } = await this._readChunk({
                 chunk: c,
                 opts,
             });
-            const feats = await this.readBamFeatures(data, cpositions, dpositions, chunk);
             const mateRecs = [];
-            for (let i = 0; i < feats.length; i += 1) {
-                const feature = feats[i];
+            for (const feature of await this.readBamFeatures(data, cpositions, dpositions, chunk)) {
                 if (unmatedPairs[feature.get('name')] && !readIds[feature.id()]) {
                     mateRecs.push(feature);
                 }
             }
             return mateRecs;
-        });
-        return flat(await Promise.all(mateFeatPromises));
+        }));
+        return mateFeatPromises.flat();
+    }
+    async _readRegion(position, size, opts = {}) {
+        const { bytesRead, buffer } = await this.bam.read(Buffer.alloc(size), 0, size, position, opts);
+        return buffer.subarray(0, Math.min(bytesRead, size));
     }
     async _readChunk({ chunk, opts }) {
-        const size = chunk.fetchedSize();
-        const { buffer, bytesRead } = await this.bam.read(Buffer.alloc(size), 0, size, chunk.minv.blockPosition, opts);
-        const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buffer.subarray(0, Math.min(bytesRead, size)), chunk);
+        const buffer = await this._readRegion(chunk.minv.blockPosition, chunk.fetchedSize(), opts);
+        const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buffer, chunk);
         return { data, cpositions, dpositions, chunk };
     }
     async readBamFeatures(ba, cpositions, dpositions, chunk) {
@@ -321,23 +309,27 @@ export default class BamFile {
                         start: blockStart,
                         end: blockEnd,
                     },
-                    // the below results in an automatically calculated file-offset based ID
-                    // if the info for that is available, otherwise crc32 of the features
+                    // the below results in an automatically calculated file-offset based
+                    // ID if the info for that is available, otherwise crc32 of the
+                    // features
                     //
-                    // cpositions[pos] refers to actual file offset of a bgzip block boundaries
+                    // cpositions[pos] refers to actual file offset of a bgzip block
+                    // boundaries
                     //
-                    // we multiply by (1 <<8) in order to make sure each block has a "unique"
-                    // address space so that data in that block could never overlap
+                    // we multiply by (1 <<8) in order to make sure each block has a
+                    // "unique" address space so that data in that block could never
+                    // overlap
                     //
                     // then the blockStart-dpositions is an uncompressed file offset from
-                    // that bgzip block boundary, and since the cpositions are multiplied by
-                    // (1 << 8) these uncompressed offsets get a unique space
+                    // that bgzip block boundary, and since the cpositions are multiplied
+                    // by (1 << 8) these uncompressed offsets get a unique space
                     //
-                    // this has an extra chunk.minv.dataPosition added on because it blockStart
-                    // starts at 0 instead of chunk.minv.dataPosition
+                    // this has an extra chunk.minv.dataPosition added on because it
+                    // blockStart starts at 0 instead of chunk.minv.dataPosition
                     //
-                    // the +1 is just to avoid any possible uniqueId 0 but this does not realistically happen
-                    fileOffset: cpositions
+                    // the +1 is just to avoid any possible uniqueId 0 but this does not
+                    // realistically happen
+                    fileOffset: cpositions.length > 0
                         ? cpositions[pos] * (1 << 8) +
                             (blockStart - dpositions[pos]) +
                             chunk.minv.dataPosition +
@@ -356,22 +348,34 @@ export default class BamFile {
         return sink;
     }
     async hasRefSeq(seqName) {
-        const refId = this.chrToIndex && this.chrToIndex[seqName];
-        return this.index.hasRefSeq(refId);
+        var _a, _b;
+        const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
+        return seqId === undefined ? false : (_b = this.index) === null || _b === void 0 ? void 0 : _b.hasRefSeq(seqId);
     }
     async lineCount(seqName) {
-        const refId = this.chrToIndex && this.chrToIndex[seqName];
-        return this.index.lineCount(refId);
+        var _a;
+        const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
+        return seqId === undefined || !this.index ? 0 : this.index.lineCount(seqId);
     }
     async indexCov(seqName, start, end) {
+        var _a;
+        if (!this.index) {
+            return [];
+        }
         await this.index.parse();
-        const seqId = this.chrToIndex && this.chrToIndex[seqName];
-        return this.index.indexCov(seqId, start, end);
+        const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
+        return seqId === undefined ? [] : this.index.indexCov(seqId, start, end);
     }
     async blocksForRange(seqName, start, end, opts) {
+        var _a;
+        if (!this.index) {
+            return [];
+        }
         await this.index.parse();
-        const seqId = this.chrToIndex && this.chrToIndex[seqName];
-        return this.index.blocksForRange(seqId, start, end, opts);
+        const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
+        return seqId === undefined
+            ? []
+            : this.index.blocksForRange(seqId, start, end, opts);
     }
 }
 //# sourceMappingURL=bamFile.js.map

package/esm/bamFile.js.map

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

@@ -1,16 +1,12 @@
+/// <reference types="node" />
 import VirtualOffset from './virtualOffset';
 export default class Chunk {
     minv: VirtualOffset;
     maxv: VirtualOffset;
     bin: number;
-    _fetchedSize?: number;
-    /**
-     * @param {VirtualOffset} minv
-     * @param {VirtualOffset} maxv
-     * @param {number} bin
-     * @param {number} [fetchedSize]
-     */
-    constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?: undefined);
+    _fetchedSize?: number | undefined;
+    buffer?: Buffer;
+    constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, _fetchedSize?: number | undefined);
     toUniqueString(): string;
     toString(): string;
     compareTo(b: Chunk): number;

package/esm/chunk.js

@@ -1,16 +1,10 @@
 // little class representing a chunk in the index
 export default class Chunk {
-    /**
-     * @param {VirtualOffset} minv
-     * @param {VirtualOffset} maxv
-     * @param {number} bin
-     * @param {number} [fetchedSize]
-     */
-    constructor(minv, maxv, bin, fetchedSize = undefined) {
+    constructor(minv, maxv, bin, _fetchedSize) {
         this.minv = minv;
         this.maxv = maxv;
         this.bin = bin;
-        this._fetchedSize = fetchedSize;
+        this._fetchedSize = _fetchedSize;
     }
     toUniqueString() {
         return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;

package/esm/chunk.js.map

@@ -1 +1 @@
-{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAMxB;;;;;OAKG;IACH,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,SAAS;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,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,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE;YACnC,OAAO,IAAI,CAAC,YAAY,CAAA;SACzB;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}
+{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAGxB,YACS,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAe;QACnB,SAAI,GAAJ,IAAI,CAAe;QACnB,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,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,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE;YACnC,OAAO,IAAI,CAAC,YAAY,CAAA;SACzB;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}

package/esm/csi.d.ts

@@ -1,4 +1,5 @@
 /// <reference types="node" />
+import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 import { BaseOpts } from './util';
 import IndexFile from './indexFile';
@@ -6,30 +7,93 @@ export default class CSI extends IndexFile {
     private maxBinNumber;
     private depth;
     private minShift;
-    constructor(args: any);
-    lineCount(refId: number): Promise<number>;
+    setupP?: ReturnType<CSI['_parse']>;
+    lineCount(refId: number, opts?: BaseOpts): Promise<number>;
     indexCov(): Promise<never[]>;
-    parseAuxData(bytes: Buffer, offset: number, auxLength: number): {
-        [key: string]: any;
-    };
-    _parseNameBytes(namesBytes: Buffer): {
+    parseAuxData(bytes: Buffer, offset: number): {
         refNameToId: {
             [key: string]: number;
         };
         refIdToName: string[];
+        columnNumbers: {
+            ref: number;
+            start: number;
+            end: number;
+        };
+        coordinateType: string;
+        metaValue: number;
+        metaChar: string;
+        skipLines: number;
+        format: string;
+        formatFlags: number;
     };
     _parse(opts: {
         signal?: AbortSignal;
     }): Promise<{
-        [key: string]: any;
+        refNameToId?: {
+            [key: string]: number;
+        } | undefined;
+        refIdToName?: string[] | undefined;
+        columnNumbers?: {
+            ref: number;
+            start: number;
+            end: number;
+        } | undefined;
+        coordinateType?: string | undefined;
+        metaValue?: number | undefined;
+        metaChar?: string | undefined;
+        skipLines?: number | undefined;
+        format?: string | undefined;
+        formatFlags?: number | undefined;
+        csiVersion: number;
+        firstDataLine: VirtualOffset | undefined;
+        indices: {
+            binIndex: {
+                [key: string]: Chunk[];
+            };
+            stats?: {
+                lineCount: number;
+            } | undefined;
+        }[];
+        refCount: number;
+        csi: boolean;
+        maxBlockSize: number;
     }>;
-    parsePseudoBin(bytes: Buffer, offset: number): {
-        lineCount: number;
-    };
     blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
     /**
      * calculate the list of bins that may overlap with region [beg,end)
      * (zero-based half-open)
      */
     reg2bins(beg: number, end: number): number[][];
+    parse(opts?: BaseOpts): Promise<{
+        refNameToId?: {
+            [key: string]: number;
+        } | undefined;
+        refIdToName?: string[] | undefined;
+        columnNumbers?: {
+            ref: number;
+            start: number;
+            end: number;
+        } | undefined;
+        coordinateType?: string | undefined;
+        metaValue?: number | undefined;
+        metaChar?: string | undefined;
+        skipLines?: number | undefined;
+        format?: string | undefined;
+        formatFlags?: number | undefined;
+        csiVersion: number;
+        firstDataLine: VirtualOffset | undefined;
+        indices: {
+            binIndex: {
+                [key: string]: Chunk[];
+            };
+            stats?: {
+                lineCount: number;
+            } | undefined;
+        }[];
+        refCount: number;
+        csi: boolean;
+        maxBlockSize: number;
+    }>;
+    hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
 }