@gmod/bam 1.1.18 → 2.0.1

package/dist/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>;
 }

package/dist/csi.js

@@ -35,7 +35,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const long_1 = __importDefault(require("long"));
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const virtualOffset_1 = __importStar(require("./virtualOffset"));
 const chunk_1 = __importDefault(require("./chunk"));
@@ -50,27 +49,17 @@ function rshift(num, bits) {
     return Math.floor(num / Math.pow(2, bits));
 }
 class CSI extends indexFile_1.default {
-    constructor(args) {
-        super(args);
+    constructor() {
+        super(...arguments);
         this.maxBinNumber = 0;
         this.depth = 0;
         this.minShift = 0;
     }
-    lineCount(refId) {
+    lineCount(refId, opts) {
+        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
-            const indexData = yield 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;
+            const indexData = yield 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;
         });
     }
     indexCov() {
@@ -78,61 +67,42 @@ class CSI extends indexFile_1.default {
             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}`);
+    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}`);
         }
-        data.columnNumbers = {
+        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 Object.assign({ columnNumbers,
+            coordinateType,
+            metaValue,
+            metaChar,
+            skipLines,
+            format,
+            formatFlags }, (0, util_1.parseNameBytes)(bytes.subarray(offset + 28, offset + 28 + nameSectionLength), this.renameRefSeq));
     }
     // fetch and parse the index
     _parse(opts) {
         return __awaiter(this, void 0, void 0, function* () {
-            const data = { csi: true, maxBlockSize: 1 << 16 };
-            const buffer = (yield this.filehandle.readFile(opts));
+            const buffer = yield this.filehandle.readFile(opts);
             const bytes = yield (0, bgzf_filehandle_1.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');
@@ -142,53 +112,50 @@ class CSI extends indexFile_1.default {
             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) {
-                yield (0, util_1.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 = (0, util_1.parsePseudoBin)(bytes, curr + 28);
+                        curr += 28 + 16;
                     }
                     else {
-                        const loffset = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 4);
-                        this._findFirstData(data, loffset);
-                        const chunkCount = bytes.readInt32LE(currOffset + 12);
-                        currOffset += 16;
+                        firstDataLine = (0, util_1.findFirstData)(firstDataLine, (0, virtualOffset_1.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 = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
-                            const v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
-                            currOffset += 16;
-                            // this._findFirstData(data, u)
+                            const u = (0, virtualOffset_1.fromBytes)(bytes, curr);
+                            curr += 8;
+                            const v = (0, virtualOffset_1.fromBytes)(bytes, curr);
+                            curr += 8;
+                            firstDataLine = (0, util_1.findFirstData)(firstDataLine, u);
                             chunks[k] = new chunk_1.default(u, v, bin);
                         }
                         binIndex[bin] = chunks;
                     }
                 }
-                data.indices[i] = { binIndex, stats };
+                indices[i] = { binIndex, stats };
             }
-            return data;
+            return Object.assign({ csiVersion,
+                firstDataLine,
+                indices,
+                refCount, csi: true, maxBlockSize: 1 << 16 }, aux);
         });
     }
-    parsePseudoBin(bytes, offset) {
-        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset + 28, offset + 36), true));
-        return { lineCount };
-    }
     blocksForRange(refId, min, max, opts = {}) {
         return __awaiter(this, void 0, void 0, function* () {
             if (min < 0) {
@@ -199,15 +166,18 @@ class CSI extends indexFile_1.default {
             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_1.default(binChunks[c].minv, binChunks[c].maxv, bin));
+                        for (const c of binChunks) {
+                            chunks.push(c);
                         }
                     }
                 }
@@ -242,6 +212,24 @@ class CSI extends indexFile_1.default {
         }
         return bins;
     }
+    parse(opts = {}) {
+        return __awaiter(this, void 0, void 0, function* () {
+            if (!this.setupP) {
+                this.setupP = this._parse(opts).catch(e => {
+                    this.setupP = undefined;
+                    throw e;
+                });
+            }
+            return this.setupP;
+        });
+    }
+    hasRefSeq(seqId, opts = {}) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function* () {
+            const header = yield this.parse(opts);
+            return !!((_a = header.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
+        });
+    }
 }
 exports.default = CSI;
 //# sourceMappingURL=csi.js.map

package/dist/csi.js.map

@@ -1 +1 @@
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+{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAC7C,iEAA0D;AAC1D,oDAA2B;AAC3B,iCAMe;AAEf,4DAAmC;AAEnC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,mBAAS;IAA1C;;QACU,iBAAY,GAAG,CAAC,CAAA;QAChB,UAAK,GAAG,CAAC,CAAA;QACT,aAAQ,GAAG,CAAC,CAAA;IA+MtB,CAAC;IA3MO,SAAS,CAAC,KAAa,EAAE,IAAe;;;YAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,OAAO,CAAA,MAAA,MAAA,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,KAAK,0CAAE,SAAS,KAAI,CAAC,CAAA;;KACvD;IAEK,QAAQ;;YACZ,OAAO,EAAE,CAAA;QACX,CAAC;KAAA;IAED,YAAY,CAAC,KAAa,EAAE,MAAc;QACxC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GACV,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAGnC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACpB,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,uBACE,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW,IACR,IAAA,qBAAc,EACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB,EACF;IACH,CAAC;IAED,4BAA4B;IACtB,MAAM,CAAC,IAA8B;;YACzC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;YACnD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;YAEjC,IAAI,UAAU,CAAA;YACd,0BAA0B;YAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE,CAAC;gBACzC,UAAU,GAAG,CAAC,CAAA;YAChB,CAAC;iBAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE,CAAC;gBAChD,UAAU,GAAG,CAAC,CAAA;YAChB,CAAC;iBAAM,CAAC;gBACN,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;gBACjC,oDAAoD;YACtD,CAAC;YAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACjC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YAC3D,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACvC,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;YACtE,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;YAIlD,+CAA+C;YAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;YAC7B,IAAI,aAAwC,CAAA;YAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAGtB,QAAQ,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACxC,IAAI,IAAI,CAAC,CAAA;gBACT,MAAM,QAAQ,GAA+B,EAAE,CAAA;gBAC/C,IAAI,KAAK,CAAA,CAAC,iDAAiD;gBAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;oBAClC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,CAAA;oBACpC,IAAI,IAAI,CAAC,CAAA;oBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;wBAC5B,KAAK,GAAG,IAAA,qBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;wBACxC,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;oBACjB,CAAC;yBAAM,CAAC;wBACN,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;wBACpE,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;wBAC1C,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;wBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;4BACvC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,CAAA;4BACT,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,CAAA;4BACT,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;4BAC/C,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;wBAClC,CAAC;wBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;oBACxB,CAAC;gBACH,CAAC;gBAED,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;YAClC,CAAC;YAED,uBACE,UAAU;gBACV,aAAa;gBACb,OAAO;gBACP,QAAQ,EACR,GAAG,EAAE,IAAI,EACT,YAAY,EAAE,CAAC,IAAI,EAAE,IAClB,GAAG,EACP;QACH,CAAC;KAAA;IAEK,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;;YAEnB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,GAAG,GAAG,CAAC,CAAA;YACT,CAAC;YAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,MAAM,EAAE,GAAG,SAAS,aAAT,SAAS,uBAAT,SAAS,CAAE,OAAO,CAAC,KAAK,CAAC,CAAA;YACpC,IAAI,CAAC,EAAE,EAAE,CAAC;gBACR,OAAO,EAAE,CAAA;YACX,CAAC;YACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;YAE/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBA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package/dist/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/dist/htsget.js

@@ -53,13 +53,14 @@ var __asyncValues = (this && this.__asyncValues) || function (o) {
 var __asyncDelegator = (this && this.__asyncDelegator) || function (o) {
     var i, p;
     return i = {}, verb("next"), verb("throw", function (e) { throw e; }), verb("return"), i[Symbol.iterator] = function () { return this; }, i;
-    function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: n === "return" } : f ? f(v) : v; } : f; }
+    function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: false } : f ? f(v) : v; } : f; }
 };
 var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _arguments, generator) {
     if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
     var g = generator.apply(thisArg, _arguments || []), i, q = [];
-    return i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i;
-    function verb(n) { if (g[n]) i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; }
+    return i = {}, verb("next"), verb("throw"), verb("return", awaitReturn), i[Symbol.asyncIterator] = function () { return this; }, i;
+    function awaitReturn(f) { return function (v) { return Promise.resolve(v).then(f, reject); }; }
+    function verb(n, f) { if (g[n]) { i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; if (f) i[n] = f(i[n]); } }
     function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }
     function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }
     function fulfill(value) { resume("next", value); }
@@ -67,72 +68,93 @@ var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _ar
     function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const bamFile_1 = __importStar(require("./bamFile"));
-require("cross-fetch/polyfill");
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const buffer_1 = require("buffer");
+const bamFile_1 = __importStar(require("./bamFile"));
 const sam_1 = require("./sam");
 function concat(arr, opts) {
     return __awaiter(this, void 0, void 0, function* () {
         const res = yield Promise.all(arr.map((chunk) => __awaiter(this, void 0, void 0, function* () {
             const { url, headers } = chunk;
             if (url.startsWith('data:')) {
-                return Buffer.from(url.split(',')[1], 'base64');
+                return buffer_1.Buffer.from(url.split(',')[1], 'base64');
             }
             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 } = headers, rest = __rest(headers, ["referer"]);
-                const res = yield fetch(url, Object.assign(Object.assign({}, opts), { headers: Object.assign(Object.assign({}, opts.headers), rest) }));
+                const res = yield fetch(url, Object.assign(Object.assign({}, opts), { headers: Object.assign(Object.assign({}, 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}: ${yield res.text()}`);
                 }
-                return Buffer.from(yield res.arrayBuffer());
+                return buffer_1.Buffer.from(yield res.arrayBuffer());
             }
         })));
-        return Buffer.concat(yield Promise.all(res.map(elt => (0, bgzf_filehandle_1.unzip)(elt))));
+        return buffer_1.Buffer.concat(yield Promise.all(res.map(elt => (0, bgzf_filehandle_1.unzip)(elt))));
     });
 }
 class HtsgetFile extends bamFile_1.default {
     constructor(args) {
-        // @ts-ignore override bam defaults
-        super({ bamFilehandle: '?', baiFilehandle: '?' });
+        super({ htsget: true });
         this.baseUrl = args.baseUrl;
         this.trackId = args.trackId;
     }
-    streamRecordsForRange(chr, min, max, opts = {
-        viewAsPairs: false,
-        pairAcrossChr: false,
-        maxInsertSize: 200000,
-    }) {
+    streamRecordsForRange(chr, min, max, opts) {
+        var _a;
         return __asyncGenerator(this, arguments, function* streamRecordsForRange_1() {
             const base = `${this.baseUrl}/${this.trackId}`;
             const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
-            const chrId = this.chrToIndex && this.chrToIndex[chr];
-            const result = yield __await(fetch(url, Object.assign({}, 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 yield __await([]);
+            }
+            else {
+                const result = yield __await(fetch(url, Object.assign({}, opts)));
+                if (!result.ok) {
+                    throw new Error(`HTTP ${result.status} fetching ${url}: ${yield __await(result.text())}`);
+                }
+                const data = yield __await(result.json());
+                const uncba = yield __await(concat(data.htsget.urls.slice(1), opts));
+                yield __await(yield* __asyncDelegator(__asyncValues(this._fetchChunkFeatures([
+                    // fake stuff to pretend to be a Chunk
+                    {
+                        buffer: uncba,
+                        _fetchedSize: undefined,
+                        bin: 0,
+                        compareTo() {
+                            return 0;
+                        },
+                        toUniqueString() {
+                            return `${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}_${max}`;
+                        },
+                    },
+                ], chrId, min, max, opts))));
             }
-            const data = yield __await(result.json());
-            const uncba = yield __await(concat(data.htsget.urls.slice(1), opts));
-            const chunk = {
-                buffer: uncba,
-                chunk: { minv: { dataPosition: 0 } },
-                toString() {
-                    return `${chr}_${min}_${max}`;
-                },
-            };
-            yield __await(yield* __asyncDelegator(__asyncValues(this._fetchChunkFeatures(
-            // @ts-ignore
-            [chunk], chrId, min, max, opts))));
         });
     }
-    //@ts-ignore
-    _readChunk(params) {
+    _readChunk({ chunk }) {
         return __awaiter(this, void 0, void 0, function* () {
-            const { chunk } = params;
-            const { buffer, chunk: c2 } = chunk;
-            return { data: buffer, cpositions: null, dpositions: null, chunk: c2 };
+            if (!chunk.buffer) {
+                throw new Error('expected chunk.buffer in htsget');
+            }
+            return { data: chunk.buffer, cpositions: [], dpositions: [], chunk };
         });
     }
     getHeader(opts = {}) {
@@ -140,7 +162,7 @@ class HtsgetFile extends bamFile_1.default {
             const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
             const result = yield fetch(url, opts);
             if (!result.ok) {
-                throw new Error(`Failed to fetch ${result.statusText}`);
+                throw new Error(`HTTP ${result.status} fetching ${url}: ${yield result.text()}`);
             }
             const data = yield result.json();
             const uncba = yield concat(data.htsget.urls, opts);
@@ -154,17 +176,21 @@ class HtsgetFile extends bamFile_1.default {
             // 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;