@gmod/bam 1.1.18 → 2.0.0

package/esm/csi.js

@@ -1,8 +1,7 @@
-import Long from 'long';
 import { unzip } from '@gmod/bgzf-filehandle';
 import VirtualOffset, { fromBytes } from './virtualOffset';
 import Chunk from './chunk';
-import { longToNumber, abortBreakPoint, optimizeChunks } from './util';
+import { optimizeChunks, findFirstData, parsePseudoBin, parseNameBytes, } from './util';
 import IndexFile from './indexFile';
 const CSI1_MAGIC = 21582659; // CSI\1
 const CSI2_MAGIC = 38359875; // CSI\2
@@ -13,84 +12,58 @@ function rshift(num, bits) {
     return Math.floor(num / 2 ** bits);
 }
 export default class CSI extends IndexFile {
-    constructor(args) {
-        super(args);
+    constructor() {
+        super(...arguments);
         this.maxBinNumber = 0;
         this.depth = 0;
         this.minShift = 0;
     }
-    async lineCount(refId) {
-        const indexData = await this.parse();
-        if (!indexData) {
-            return -1;
-        }
-        const idx = indexData.indices[refId];
-        if (!idx) {
-            return -1;
-        }
-        const { stats } = indexData.indices[refId];
-        if (stats) {
-            return stats.lineCount;
-        }
-        return -1;
+    async lineCount(refId, opts) {
+        var _a, _b;
+        const indexData = await this.parse(opts);
+        return ((_b = (_a = indexData.indices[refId]) === null || _a === void 0 ? void 0 : _a.stats) === null || _b === void 0 ? void 0 : _b.lineCount) || 0;
     }
     async indexCov() {
         return [];
     }
-    parseAuxData(bytes, offset, auxLength) {
-        if (auxLength < 30) {
-            return {};
-        }
-        const data = {};
-        data.formatFlags = bytes.readInt32LE(offset);
-        data.coordinateType =
-            data.formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
-        data.format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[data.formatFlags & 0xf];
-        if (!data.format) {
-            throw new Error(`invalid Tabix preset format flags ${data.formatFlags}`);
-        }
-        data.columnNumbers = {
+    parseAuxData(bytes, offset) {
+        const formatFlags = bytes.readInt32LE(offset);
+        const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
+        const format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[formatFlags & 0xf];
+        if (!format) {
+            throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
+        }
+        const columnNumbers = {
             ref: bytes.readInt32LE(offset + 4),
             start: bytes.readInt32LE(offset + 8),
             end: bytes.readInt32LE(offset + 12),
         };
-        data.metaValue = bytes.readInt32LE(offset + 16);
-        data.metaChar = data.metaValue ? String.fromCharCode(data.metaValue) : '';
-        data.skipLines = bytes.readInt32LE(offset + 20);
+        const metaValue = bytes.readInt32LE(offset + 16);
+        const metaChar = metaValue ? String.fromCharCode(metaValue) : '';
+        const skipLines = bytes.readInt32LE(offset + 20);
         const nameSectionLength = bytes.readInt32LE(offset + 24);
-        Object.assign(data, this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength)));
-        return data;
-    }
-    _parseNameBytes(namesBytes) {
-        let currRefId = 0;
-        let currNameStart = 0;
-        const refIdToName = [];
-        const refNameToId = {};
-        for (let i = 0; i < namesBytes.length; i += 1) {
-            if (!namesBytes[i]) {
-                if (currNameStart < i) {
-                    let refName = namesBytes.toString('utf8', currNameStart, i);
-                    refName = this.renameRefSeq(refName);
-                    refIdToName[currRefId] = refName;
-                    refNameToId[refName] = currRefId;
-                }
-                currNameStart = i + 1;
-                currRefId += 1;
-            }
-        }
-        return { refNameToId, refIdToName };
+        return {
+            columnNumbers,
+            coordinateType,
+            metaValue,
+            metaChar,
+            skipLines,
+            format,
+            formatFlags,
+            ...parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength), this.renameRefSeq),
+        };
     }
     // fetch and parse the index
     async _parse(opts) {
-        const data = { csi: true, maxBlockSize: 1 << 16 };
-        const buffer = (await this.filehandle.readFile(opts));
+        const buffer = await this.filehandle.readFile(opts);
         const bytes = await unzip(buffer);
+        let csiVersion;
         // check TBI magic numbers
         if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
-            data.csiVersion = 1;
+            csiVersion = 1;
         }
         else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
-            data.csiVersion = 2;
+            csiVersion = 2;
         }
         else {
             throw new Error('Not a CSI file');
@@ -100,51 +73,53 @@ export default class CSI extends IndexFile {
         this.depth = bytes.readInt32LE(8);
         this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
         const auxLength = bytes.readInt32LE(12);
-        if (auxLength) {
-            Object.assign(data, this.parseAuxData(bytes, 16, auxLength));
-        }
-        data.refCount = bytes.readInt32LE(16 + auxLength);
+        const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined;
+        const refCount = bytes.readInt32LE(16 + auxLength);
         // read the indexes for each reference sequence
-        data.indices = new Array(data.refCount);
-        let currOffset = 16 + auxLength + 4;
-        for (let i = 0; i < data.refCount; i += 1) {
-            await abortBreakPoint(opts.signal);
+        let curr = 16 + auxLength + 4;
+        let firstDataLine;
+        const indices = new Array(refCount);
+        for (let i = 0; i < refCount; i++) {
             // the binning index
-            const binCount = bytes.readInt32LE(currOffset);
-            currOffset += 4;
+            const binCount = bytes.readInt32LE(curr);
+            curr += 4;
             const binIndex = {};
             let stats; // < provided by parsing a pseudo-bin, if present
-            for (let j = 0; j < binCount; j += 1) {
-                const bin = bytes.readUInt32LE(currOffset);
+            for (let j = 0; j < binCount; j++) {
+                const bin = bytes.readUInt32LE(curr);
+                curr += 4;
                 if (bin > this.maxBinNumber) {
-                    // this is a fake bin that actually has stats information
-                    // about the reference sequence in it
-                    stats = this.parsePseudoBin(bytes, currOffset + 4);
-                    currOffset += 4 + 8 + 4 + 16 + 16;
+                    stats = parsePseudoBin(bytes, curr + 28);
+                    curr += 28 + 16;
                 }
                 else {
-                    const loffset = fromBytes(bytes, currOffset + 4);
-                    this._findFirstData(data, loffset);
-                    const chunkCount = bytes.readInt32LE(currOffset + 12);
-                    currOffset += 16;
+                    firstDataLine = findFirstData(firstDataLine, fromBytes(bytes, curr));
+                    curr += 8;
+                    const chunkCount = bytes.readInt32LE(curr);
+                    curr += 4;
                     const chunks = new Array(chunkCount);
                     for (let k = 0; k < chunkCount; k += 1) {
-                        const u = fromBytes(bytes, currOffset);
-                        const v = fromBytes(bytes, currOffset + 8);
-                        currOffset += 16;
-                        // this._findFirstData(data, u)
+                        const u = fromBytes(bytes, curr);
+                        curr += 8;
+                        const v = fromBytes(bytes, curr);
+                        curr += 8;
+                        firstDataLine = findFirstData(firstDataLine, u);
                         chunks[k] = new Chunk(u, v, bin);
                     }
                     binIndex[bin] = chunks;
                 }
             }
-            data.indices[i] = { binIndex, stats };
-        }
-        return data;
-    }
-    parsePseudoBin(bytes, offset) {
-        const lineCount = longToNumber(Long.fromBytesLE(Array.prototype.slice.call(bytes, offset + 28, offset + 36), true));
-        return { lineCount };
+            indices[i] = { binIndex, stats };
+        }
+        return {
+            csiVersion,
+            firstDataLine,
+            indices,
+            refCount,
+            csi: true,
+            maxBlockSize: 1 << 16,
+            ...aux,
+        };
     }
     async blocksForRange(refId, min, max, opts = {}) {
         if (min < 0) {
@@ -155,15 +130,18 @@ export default class CSI extends IndexFile {
         if (!ba) {
             return [];
         }
-        const overlappingBins = this.reg2bins(min, max); // List of bin #s that overlap min, max
+        const overlappingBins = this.reg2bins(min, max);
+        if (overlappingBins.length === 0) {
+            return [];
+        }
         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++) {
                 if (ba.binIndex[bin]) {
                     const binChunks = ba.binIndex[bin];
-                    for (let c = 0; c < binChunks.length; ++c) {
-                        chunks.push(new Chunk(binChunks[c].minv, binChunks[c].maxv, bin));
+                    for (const c of binChunks) {
+                        chunks.push(c);
                     }
                 }
             }
@@ -197,5 +175,19 @@ export default class CSI extends IndexFile {
         }
         return bins;
     }
+    async parse(opts = {}) {
+        if (!this.setupP) {
+            this.setupP = this._parse(opts).catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
+    }
+    async hasRefSeq(seqId, opts = {}) {
+        var _a;
+        const header = await this.parse(opts);
+        return !!((_a = header.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
+    }
 }
 //# sourceMappingURL=csi.js.map

package/esm/csi.js.map

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

@@ -1,7 +1,7 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 import { BaseOpts, BamOpts } from './util';
 import BamFile from './bamFile';
-import 'cross-fetch/polyfill';
 import Chunk from './chunk';
 export default class HtsgetFile extends BamFile {
     private baseUrl;
@@ -11,16 +11,13 @@ export default class HtsgetFile extends BamFile {
         baseUrl: string;
     });
     streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<import("./record").default[], void, unknown>;
-    _readChunk(params: {
-        chunk: {
-            buffer: Buffer;
-            chunk: Chunk;
-        };
+    _readChunk({ chunk }: {
+        chunk: Chunk;
         opts: BaseOpts;
     }): Promise<{
         data: Buffer;
-        cpositions: null;
-        dpositions: null;
+        cpositions: never[];
+        dpositions: never[];
         chunk: Chunk;
     }>;
     getHeader(opts?: BaseOpts): Promise<{

package/esm/htsget.js

@@ -1,6 +1,6 @@
-import BamFile, { BAM_MAGIC } from './bamFile';
-import 'cross-fetch/polyfill';
 import { unzip } from '@gmod/bgzf-filehandle';
+import { Buffer } from 'buffer';
+import BamFile, { BAM_MAGIC } from './bamFile';
 import { parseHeaderText } from './sam';
 async function concat(arr, opts) {
     const res = await Promise.all(arr.map(async (chunk) => {
@@ -10,15 +10,15 @@ async function concat(arr, opts) {
         }
         else {
             //remove referer header, it is not even allowed to be specified
-            //@ts-ignore
+            // @ts-expect-error
             //eslint-disable-next-line @typescript-eslint/no-unused-vars
             const { referer, ...rest } = headers;
             const res = await fetch(url, {
                 ...opts,
-                headers: { ...opts.headers, ...rest },
+                headers: { ...opts === null || opts === void 0 ? void 0 : opts.headers, ...rest },
             });
             if (!res.ok) {
-                throw new Error(`Failed to fetch ${res.statusText}`);
+                throw new Error(`HTTP ${res.status} fetching ${url}: ${await res.text()}`);
             }
             return Buffer.from(await res.arrayBuffer());
         }
@@ -27,47 +27,68 @@ async function concat(arr, opts) {
 }
 export default class HtsgetFile extends BamFile {
     constructor(args) {
-        // @ts-ignore override bam defaults
-        super({ bamFilehandle: '?', baiFilehandle: '?' });
+        super({ htsget: true });
         this.baseUrl = args.baseUrl;
         this.trackId = args.trackId;
     }
-    async *streamRecordsForRange(chr, min, max, opts = {
-        viewAsPairs: false,
-        pairAcrossChr: false,
-        maxInsertSize: 200000,
-    }) {
+    async *streamRecordsForRange(chr, min, max, opts) {
+        var _a;
         const base = `${this.baseUrl}/${this.trackId}`;
         const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
-        const chrId = this.chrToIndex && this.chrToIndex[chr];
-        const result = await fetch(url, { ...opts });
-        if (!result.ok) {
-            throw new Error(result.statusText);
+        const chrId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[chr];
+        if (chrId === undefined) {
+            yield [];
+        }
+        else {
+            const result = await fetch(url, { ...opts });
+            if (!result.ok) {
+                throw new Error(`HTTP ${result.status} fetching ${url}: ${await result.text()}`);
+            }
+            const data = await result.json();
+            const uncba = await concat(data.htsget.urls.slice(1), opts);
+            yield* this._fetchChunkFeatures([
+                // fake stuff to pretend to be a Chunk
+                {
+                    buffer: uncba,
+                    _fetchedSize: undefined,
+                    bin: 0,
+                    compareTo() {
+                        return 0;
+                    },
+                    toUniqueString() {
+                        return `${chr}_${min}_${max}`;
+                    },
+                    fetchedSize() {
+                        return 0;
+                    },
+                    minv: {
+                        dataPosition: 0,
+                        blockPosition: 0,
+                        compareTo: () => 0,
+                    },
+                    maxv: {
+                        dataPosition: Number.MAX_SAFE_INTEGER,
+                        blockPosition: 0,
+                        compareTo: () => 0,
+                    },
+                    toString() {
+                        return `${chr}_${min}_${max}`;
+                    },
+                },
+            ], chrId, min, max, opts);
         }
-        const data = await result.json();
-        const uncba = await concat(data.htsget.urls.slice(1), opts);
-        const chunk = {
-            buffer: uncba,
-            chunk: { minv: { dataPosition: 0 } },
-            toString() {
-                return `${chr}_${min}_${max}`;
-            },
-        };
-        yield* this._fetchChunkFeatures(
-        // @ts-ignore
-        [chunk], chrId, min, max, opts);
     }
-    //@ts-ignore
-    async _readChunk(params) {
-        const { chunk } = params;
-        const { buffer, chunk: c2 } = chunk;
-        return { data: buffer, cpositions: null, dpositions: null, chunk: c2 };
+    async _readChunk({ chunk }) {
+        if (!chunk.buffer) {
+            throw new Error('expected chunk.buffer in htsget');
+        }
+        return { data: chunk.buffer, cpositions: [], dpositions: [], chunk };
     }
     async getHeader(opts = {}) {
         const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
         const result = await fetch(url, opts);
         if (!result.ok) {
-            throw new Error(`Failed to fetch ${result.statusText}`);
+            throw new Error(`HTTP ${result.status} fetching ${url}: ${await result.text()}`);
         }
         const data = await result.json();
         const uncba = await concat(data.htsget.urls, opts);
@@ -81,17 +102,21 @@ export default class HtsgetFile extends BamFile {
         // mapping between ref ref ID numbers and names
         const idToName = [];
         const nameToId = {};
-        const sqLines = samHeader.filter((l) => l.tag === 'SQ');
-        sqLines.forEach((sqLine, refId) => {
-            sqLine.data.forEach((item) => {
+        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') {
-                    // this is the ref name
-                    const refName = item.value;
-                    nameToId[refName] = refId;
-                    idToName[refId] = refName;
+                    refName = item.value;
                 }
-            });
-        });
+                else if (item.tag === 'LN') {
+                    length = +item.value;
+                }
+            }
+            nameToId[refName] = refId;
+            idToName[refId] = { refName, length };
+        }
         this.chrToIndex = nameToId;
         this.indexToChr = idToName;
         return samHeader;

package/esm/htsget.js.map

@@ -1 +1 @@
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+{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAE/B,OAAO,OAAO,EAAE,EAAE,SAAS,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,EAAE,eAAe,EAAE,MAAM,OAAO,CAAA;AAMvC,KAAK,UAAU,MAAM,CAAC,GAAkB,EAAE,IAA0B;IAClE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,KAAK,EAAC,EAAE;QACpB,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE;YAC3B,OAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;SAChD;aAAM;YACL,+DAA+D;YAC/D,mBAAmB;YACnB,4DAA4D;YAC5D,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,CAAA;YACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;gBAC3B,GAAG,IAAI;gBACP,OAAO,EAAE,EAAE,GAAG,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,EAAE,GAAG,IAAI,EAAE;aACvC,CAAC,CAAA;YACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE;gBACX,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAC1D,CAAA;aACF;YACD,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;SAC5C;IACH,CAAC,CAAC,CACH,CAAA;IAED,OAAO,MAAM,CAAC,MAAM,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;AACrE,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,OAAO;IAK7C,YAAY,IAA0C;QACpD,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAA;QACvB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,CAAC,qBAAqB,CAC1B,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;;QAEd,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;QAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;QAC7E,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE;YACvB,MAAM,EAAE,CAAA;SACT;aAAM;YACL,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,CAAC,CAAA;YAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;gBACd,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;aACF;YACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;YAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;YAE3D,KAAK,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAC7B;gBACE,sCAAsC;gBACtC;oBACE,MAAM,EAAE,KAAK;oBACb,YAAY,EAAE,SAAS;oBACvB,GAAG,EAAE,CAAC;oBACN,SAAS;wBACP,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,cAAc;wBACZ,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;oBACD,WAAW;wBACT,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,CAAC;wBACf,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,MAAM,CAAC,gBAAgB;wBACrC,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,QAAQ;wBACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;iBACF;aACF,EACD,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA;SACF;IACH,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,EAAE,KAAK,EAAoC;QAC1D,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;SACnD;QACD,OAAO,EAAE,IAAI,EAAE,KAAK,CAAC,MAAM,EAAE,UAAU,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE,KAAK,EAAE,CAAA;IACtE,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAiB,EAAE;QACjC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;QAC3E,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;YACd,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;SACF;QACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;QAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;YACtC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;SAClC;QACD,MAAM,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACpC,MAAM,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;QACzD,MAAM,SAAS,GAAG,eAAe,CAAC,UAAU,CAAC,CAAA;QAE7C,oDAAoD;QACpD,+CAA+C;QAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;QAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;QACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE;YAC/C,IAAI,OAAO,GAAG,EAAE,CAAA;YAChB,IAAI,MAAM,GAAG,CAAC,CAAA;YACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE;gBAC9B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;oBACrB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;iBACrB;qBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;oBAC5B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;iBACrB;aACF;YACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;SACtC;QACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,OAAO,SAAS,CAAA;IAClB,CAAC;CACF"}

package/esm/index.d.ts

@@ -1,6 +1,5 @@
-import BAI from './bai';
-import CSI from './csi';
-import BamFile from './bamFile';
-import HtsgetFile from './htsget';
-import BamRecord from './record';
-export { BAI, CSI, BamFile, BamRecord, HtsgetFile };
+export { default as BAI } from './bai';
+export { default as BamFile } from './bamFile';
+export { default as CSI } from './csi';
+export { default as BamRecord } from './record';
+export { default as HtsgetFile } from './htsget';

package/esm/index.js

@@ -1,7 +1,6 @@
-import BAI from './bai';
-import CSI from './csi';
-import BamFile from './bamFile';
-import HtsgetFile from './htsget';
-import BamRecord from './record';
-export { BAI, CSI, BamFile, BamRecord, HtsgetFile };
+export { default as BAI } from './bai';
+export { default as BamFile } from './bamFile';
+export { default as CSI } from './csi';
+export { default as BamRecord } from './record';
+export { default as HtsgetFile } from './htsget';
 //# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,OAAO,MAAM,WAAW,CAAA;AAC/B,OAAO,UAAU,MAAM,UAAU,CAAA;AACjC,OAAO,SAAS,MAAM,UAAU,CAAA;AAEhC,OAAO,EAAE,GAAG,EAAE,GAAG,EAAE,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,OAAO,CAAA;AACtC,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,WAAW,CAAA;AAC9C,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,OAAO,CAAA;AACtC,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,UAAU,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,UAAU,CAAA"}

package/esm/indexFile.d.ts

@@ -1,11 +1,9 @@
 import { GenericFilehandle } from 'generic-filehandle';
-import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 import { BaseOpts } from './util';
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
-    setupP?: Promise<any>;
     /**
      * @param {filehandle} filehandle
      * @param {function} [renameRefSeqs]
@@ -15,14 +13,10 @@ export default abstract class IndexFile {
         renameRefSeq?: (a: string) => string;
     });
     abstract lineCount(refId: number): Promise<number>;
-    protected abstract _parse(opts?: BaseOpts): Promise<any>;
     abstract indexCov(refId: number, start?: number, end?: number): Promise<{
         start: number;
         end: number;
         score: number;
     }[]>;
     abstract blocksForRange(chrId: number, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
-    _findFirstData(data: any, virtualOffset: VirtualOffset): void;
-    parse(opts?: BaseOpts): Promise<any>;
-    hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
 }

package/esm/indexFile.js

@@ -7,27 +7,5 @@ export default class IndexFile {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeq;
     }
-    _findFirstData(data, virtualOffset) {
-        const currentFdl = data.firstDataLine;
-        if (currentFdl) {
-            data.firstDataLine =
-                currentFdl.compareTo(virtualOffset) > 0 ? virtualOffset : currentFdl;
-        }
-        else {
-            data.firstDataLine = virtualOffset;
-        }
-    }
-    async parse(opts = {}) {
-        if (!this.setupP) {
-            this.setupP = this._parse(opts).catch(e => {
-                this.setupP = undefined;
-                throw e;
-            });
-        }
-        return this.setupP;
-    }
-    async hasRefSeq(seqId, opts = {}) {
-        return !!((await this.parse(opts)).indices[seqId] || {}).binIndex;
-    }
 }
 //# sourceMappingURL=indexFile.js.map

package/esm/indexFile.js.map

@@ -1 +1 @@
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+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAIA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAIrC;;;OAGG;IACH,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;CAcF"}

package/esm/nullIndex.d.ts

@@ -0,0 +1,7 @@
+import IndexFile from './indexFile';
+export default class NullIndex extends IndexFile {
+    lineCount(): Promise<any>;
+    protected _parse(): Promise<any>;
+    indexCov(): Promise<any>;
+    blocksForRange(): Promise<any>;
+}

package/esm/nullIndex.js

@@ -0,0 +1,16 @@
+import IndexFile from './indexFile';
+export default class NullIndex extends IndexFile {
+    lineCount() {
+        throw new Error('never called');
+    }
+    _parse() {
+        throw new Error('never called');
+    }
+    async indexCov() {
+        throw new Error('never called');
+    }
+    blocksForRange() {
+        throw new Error('never called');
+    }
+}
+//# sourceMappingURL=nullIndex.js.map

package/esm/nullIndex.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"nullIndex.js","sourceRoot":"","sources":["../src/nullIndex.ts"],"names":[],"mappings":"AAAA,OAAO,SAAS,MAAM,aAAa,CAAA;AAEnC,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,SAAS;IACvC,SAAS;QACd,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IACS,MAAM;QACd,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,QAAQ;QACnB,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEM,cAAc;QACnB,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;CACF"}