npm - @gmod/bam - Versions diffs - 4.0.0 → 5.0.0 - Mend

@gmod/bam 4.0.0 → 5.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (68) hide show

package/esm/bamFile.js CHANGED Viewed

@@ -1,7 +1,6 @@
-import { Buffer } from 'buffer';
 import crc32 from 'crc/crc32';
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
-import { LocalFile, RemoteFile } from 'generic-filehandle';
+import { LocalFile, RemoteFile } from 'generic-filehandle2';
 import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import QuickLRU from 'quick-lru';
 // locals
@@ -34,21 +33,29 @@ class NullFilehandle {
     }
 }
 export default class BamFile {
+    renameRefSeq;
+    bam;
+    header;
+    chrToIndex;
+    indexToChr;
+    yieldThreadTime;
+    index;
+    htsget = false;
+    headerP;
+    featureCache = new AbortablePromiseCache({
+        cache: new QuickLRU({
+            maxSize: 50,
+        }),
+        fill: async (args, signal) => {
+            const { chunk, opts } = args;
+            const { data, cpositions, dpositions } = await this._readChunk({
+                chunk,
+                opts: { ...opts, signal },
+            });
+            return this.readBamFeatures(data, cpositions, dpositions, chunk);
+        },
+    });
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime = 100, renameRefSeqs = n => n, }) {
-        this.htsget = false;
-        this.featureCache = new AbortablePromiseCache({
-            cache: new QuickLRU({
-                maxSize: 50,
-            }),
-            fill: async (args, signal) => {
-                const { chunk, opts } = args;
-                const { data, cpositions, dpositions } = await this._readChunk({
-                    chunk,
-                    opts: { ...opts, signal },
-                });
-                return this.readBamFeatures(data, cpositions, dpositions, chunk);
-            },
-        });
         this.renameRefSeq = renameRefSeqs;
         if (bamFilehandle) {
             this.bam = bamFilehandle;
@@ -110,21 +117,19 @@ export default class BamFile {
         let buffer;
         if (ret) {
             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');
-            }
-            buffer = res.buffer.subarray(0, Math.min(res.bytesRead, ret));
+            buffer = await this.bam.read(s, 0);
         }
         else {
             buffer = await this.bam.readFile(opts);
         }
         const uncba = await unzip(buffer);
-        if (uncba.readInt32LE(0) !== BAM_MAGIC) {
+        const dataView = new DataView(uncba.buffer);
+        if (dataView.getInt32(0, true) !== BAM_MAGIC) {
             throw new Error('Not a BAM file');
         }
-        const headLen = uncba.readInt32LE(4);
-        this.header = uncba.toString('utf8', 8, 8 + headLen);
+        const headLen = dataView.getInt32(4, true);
+        const decoder = new TextDecoder('utf8');
+        this.header = decoder.decode(uncba.subarray(8, 8 + headLen));
         const { chrToIndex, indexToChr } = await this._readRefSeqs(headLen + 8, 65535, opts);
         this.chrToIndex = chrToIndex;
         this.indexToChr = indexToChr;
@@ -149,20 +154,19 @@ export default class BamFile {
         if (start > refSeqBytes) {
             return this._readRefSeqs(start, refSeqBytes * 2, opts);
         }
-        const size = refSeqBytes + blockLen;
-        const { bytesRead, buffer } = await this.bam.read(Buffer.alloc(size), 0, refSeqBytes, 0, opts);
-        if (!bytesRead) {
-            throw new Error('Error reading refseqs from header');
-        }
-        const uncba = await unzip(buffer.subarray(0, Math.min(bytesRead, refSeqBytes)));
-        const nRef = uncba.readInt32LE(start);
+        // const size = refSeqBytes + blockLen <-- use this?
+        const buffer = await this.bam.read(refSeqBytes, 0, opts);
+        const uncba = await unzip(buffer);
+        const dataView = new DataView(uncba.buffer);
+        const nRef = dataView.getInt32(start, true);
         let p = start + 4;
         const chrToIndex = {};
         const indexToChr = [];
+        const decoder = new TextDecoder('utf8');
         for (let i = 0; i < nRef; i += 1) {
-            const lName = uncba.readInt32LE(p);
-            const refName = this.renameRefSeq(uncba.toString('utf8', p + 4, p + 4 + lName - 1));
-            const lRef = uncba.readInt32LE(p + lName + 4);
+            const lName = dataView.getInt32(p, true);
+            const refName = this.renameRefSeq(decoder.decode(uncba.subarray(p + 4, p + 4 + lName - 1)));
+            const lRef = dataView.getInt32(p + lName + 4, true);
             chrToIndex[refName] = i;
             indexToChr.push({ refName, length: lRef });
             p = p + 8 + lName;
@@ -177,9 +181,8 @@ export default class BamFile {
         return gen2array(this.streamRecordsForRange(chr, min, max, opts));
     }
     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];
+        const chrId = this.chrToIndex?.[chr];
         if (chrId === undefined || !this.index) {
             yield [];
         }
@@ -280,8 +283,7 @@ export default class BamFile {
         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));
+        return this.bam.read(size, position, opts);
     }
     async _readChunk({ chunk, opts }) {
         const buffer = await this._readRegion(chunk.minv.blockPosition, chunk.fetchedSize(), opts);
@@ -293,8 +295,9 @@ export default class BamFile {
         const sink = [];
         let pos = 0;
         let last = +Date.now();
+        const dataView = new DataView(ba.buffer);
         while (blockStart + 4 < ba.length) {
-            const blockSize = ba.readInt32LE(blockStart);
+            const blockSize = dataView.getInt32(blockStart, true);
             const blockEnd = blockStart + 4 + blockSize - 1;
             // increment position to the current decompressed status
             // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
@@ -336,8 +339,8 @@ export default class BamFile {
                             chunk.minv.dataPosition +
                             1
                         : // must be slice, not subarray for buffer polyfill on web
-                            // eslint-disable-next-line @typescript-eslint/no-deprecated
-                            crc32.signed(ba.slice(blockStart, blockEnd)),
+                            // @ts-expect-error
+                            crc32.signed(ba.subarray(blockStart, blockEnd)),
                 });
                 sink.push(feature);
                 if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {
@@ -350,31 +353,27 @@ export default class BamFile {
         return sink;
     }
     async hasRefSeq(seqName) {
-        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);
+        const seqId = this.chrToIndex?.[seqName];
+        return seqId === undefined ? false : this.index?.hasRefSeq(seqId);
     }
     async lineCount(seqName) {
-        var _a;
-        const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
+        const seqId = this.chrToIndex?.[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 = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
+        const seqId = this.chrToIndex?.[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 = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
+        const seqId = this.chrToIndex?.[seqName];
         return seqId === undefined
             ? []
             : this.index.blocksForRange(seqId, start, end, opts);

package/esm/bamFile.js.map CHANGED Viewed

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

@@ -4,7 +4,7 @@ export default class Chunk {
     maxv: VirtualOffset;
     bin: number;
     _fetchedSize?: number | undefined;
-    buffer?: Buffer;
+    buffer?: Uint8Array;
     constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, _fetchedSize?: number | undefined);
     toUniqueString(): string;
     toString(): string;

package/esm/chunk.js CHANGED Viewed

@@ -1,5 +1,10 @@
 // little class representing a chunk in the index
 export default class Chunk {
+    minv;
+    maxv;
+    bin;
+    _fetchedSize;
+    buffer;
     constructor(minv, maxv, bin, _fetchedSize) {
         this.minv = minv;
         this.maxv = maxv;

package/esm/chunk.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"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,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,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,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}
1	+ {"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAIf;IACA;IACA;IACA;IANF,MAAM,CAAa;IAE1B,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,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,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,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;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 CHANGED Viewed

@@ -9,7 +9,7 @@ export default class CSI extends IndexFile {
     setupP?: ReturnType<CSI['_parse']>;
     lineCount(refId: number, opts?: BaseOpts): Promise<number>;
     indexCov(): Promise<never[]>;
-    parseAuxData(bytes: Buffer, offset: number): {
+    parseAuxData(bytes: Uint8Array, offset: number): {
         refNameToId: Record<string, number>;
         refIdToName: string[];
         columnNumbers: {

package/esm/csi.js CHANGED Viewed

@@ -12,36 +12,34 @@ function rshift(num, bits) {
     return Math.floor(num / 2 ** bits);
 }
 export default class CSI extends IndexFile {
-    constructor() {
-        super(...arguments);
-        this.maxBinNumber = 0;
-        this.depth = 0;
-        this.minShift = 0;
-    }
+    maxBinNumber = 0;
+    depth = 0;
+    minShift = 0;
+    setupP;
     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;
+        return indexData.indices[refId]?.stats?.lineCount || 0;
     }
     async indexCov() {
         return [];
     }
     parseAuxData(bytes, offset) {
-        const formatFlags = bytes.readInt32LE(offset);
+        const dataView = new DataView(bytes.buffer);
+        const formatFlags = dataView.getUint32(offset, true);
         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),
+            ref: dataView.getInt32(offset + 4, true),
+            start: dataView.getInt32(offset + 8, true),
+            end: dataView.getInt32(offset + 12, true),
         };
-        const metaValue = bytes.readInt32LE(offset + 16);
+        const metaValue = dataView.getInt32(offset + 16, true);
         const metaChar = metaValue ? String.fromCharCode(metaValue) : '';
-        const skipLines = bytes.readInt32LE(offset + 20);
-        const nameSectionLength = bytes.readInt32LE(offset + 24);
+        const skipLines = dataView.getInt32(offset + 20, true);
+        const nameSectionLength = dataView.getInt32(offset + 24, true);
         return {
             columnNumbers,
             coordinateType,
@@ -57,36 +55,37 @@ export default class CSI extends IndexFile {
     async _parse(opts) {
         const buffer = await this.filehandle.readFile(opts);
         const bytes = await unzip(buffer);
+        const dataView = new DataView(bytes.buffer);
         let csiVersion;
-        // check TBI magic numbers
-        if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
+        const magic = dataView.getUint32(0, true);
+        if (magic === CSI1_MAGIC) {
             csiVersion = 1;
         }
-        else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
+        else if (magic === CSI2_MAGIC) {
             csiVersion = 2;
         }
         else {
-            throw new Error('Not a CSI file');
+            throw new Error(`Not a CSI file ${magic}`);
             // TODO: do we need to support big-endian CSI files?
         }
-        this.minShift = bytes.readInt32LE(4);
-        this.depth = bytes.readInt32LE(8);
+        this.minShift = dataView.getInt32(4, true);
+        this.depth = dataView.getInt32(8, true);
         this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
-        const auxLength = bytes.readInt32LE(12);
+        const auxLength = dataView.getInt32(12, true);
         const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined;
-        const refCount = bytes.readInt32LE(16 + auxLength);
+        const refCount = dataView.getInt32(16 + auxLength, true);
         // read the indexes for each reference sequence
         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(curr);
+            const binCount = dataView.getInt32(curr, true);
             curr += 4;
             const binIndex = {};
             let stats; // < provided by parsing a pseudo-bin, if present
             for (let j = 0; j < binCount; j++) {
-                const bin = bytes.readUInt32LE(curr);
+                const bin = dataView.getUint32(curr, true);
                 curr += 4;
                 if (bin > this.maxBinNumber) {
                     stats = parsePseudoBin(bytes, curr + 28);
@@ -95,7 +94,7 @@ export default class CSI extends IndexFile {
                 else {
                     firstDataLine = findFirstData(firstDataLine, fromBytes(bytes, curr));
                     curr += 8;
-                    const chunkCount = bytes.readInt32LE(curr);
+                    const chunkCount = dataView.getInt32(curr, true);
                     curr += 4;
                     const chunks = new Array(chunkCount);
                     for (let k = 0; k < chunkCount; k += 1) {
@@ -187,9 +186,8 @@ export default class CSI extends IndexFile {
         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);
+        return !!header.indices[seqId]?.binIndex;
     }
 }
 //# sourceMappingURL=csi.js.map

package/esm/csi.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,KAAK,MAAM,SAAS,CAAA;AAC3B,OAAO,EACL,cAAc,EACd,aAAa,EACb,cAAc,EACd,cAAc,GAEf,MAAM,QAAQ,CAAA;AAEf,OAAO,SAAS,MAAM,aAAa,CAAA;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,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAChC,YAAY,GAAG,CAAC,CAAA;IAChB,KAAK,GAAG,CAAC,CAAA;IACT,QAAQ,GAAG,CAAC,CAAA;IAEb,MAAM,CAA4B;IAEzC,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACpD,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,EACnC,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,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,OAAO;YACL,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW;YACX,GAAG,cAAc,CACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAA8B;QACzC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACnD,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,IAAI,UAAU,CAAA;QACd,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAEzC,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;YAC1C,oDAAoD;QACtD,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,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;QAC3D,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACtE,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAIxD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAGtB,QAAQ,CAAC,CAAA;QACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA,CAAC,iDAAiD;YAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,KAAK,GAAG,cAAc,CAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACxC,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;oBACpE,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;oBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBAC/C,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QAClC,CAAC;QAED,OAAO;YACL,UAAU;YACV,aAAa;YACb,OAAO;YACP,QAAQ;YACR,GAAG,EAAE,IAAI;YACT,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,GAAG,GAAG;SACP,CAAA;IACH,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;QAEnB,IAAI,GAAG,G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package/esm/htsget.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-import { Buffer } from 'buffer';
 import { BaseOpts, BamOpts } from './util';
 import BamFile from './bamFile';
 import Chunk from './chunk';
@@ -14,7 +13,7 @@ export default class HtsgetFile extends BamFile {
         chunk: Chunk;
         opts: BaseOpts;
     }): Promise<{
-        data: Buffer;
+        data: Uint8Array<ArrayBufferLike>;
         cpositions: never[];
         dpositions: never[];
         chunk: Chunk;

package/esm/htsget.js CHANGED Viewed

@@ -1,12 +1,13 @@
 import { unzip } from '@gmod/bgzf-filehandle';
-import { Buffer } from 'buffer';
+import { concatUint8Array } from './util';
 import BamFile, { BAM_MAGIC } from './bamFile';
 import { parseHeaderText } from './sam';
 async function concat(arr, opts) {
     const res = await Promise.all(arr.map(async (chunk) => {
         const { url, headers } = chunk;
         if (url.startsWith('data:')) {
-            return Buffer.from(url.split(',')[1], 'base64');
+            // @ts-expect-error
+            return Uint8Array.fromBase64(url.split(',')[1], 'base64');
         }
         else {
             //remove referer header, it is not even allowed to be specified
@@ -14,27 +15,28 @@ async function concat(arr, opts) {
             const { referer, ...rest } = headers;
             const res = await fetch(url, {
                 ...opts,
-                headers: { ...opts === null || opts === void 0 ? void 0 : opts.headers, ...rest },
+                headers: { ...opts?.headers, ...rest },
             });
             if (!res.ok) {
                 throw new Error(`HTTP ${res.status} fetching ${url}: ${await res.text()}`);
             }
-            return Buffer.from(await res.arrayBuffer());
+            return new Uint8Array(await res.arrayBuffer());
         }
     }));
-    return Buffer.concat(await Promise.all(res.map(elt => unzip(elt))));
+    return concatUint8Array(await Promise.all(res.map(elt => unzip(elt))));
 }
 export default class HtsgetFile extends BamFile {
+    baseUrl;
+    trackId;
     constructor(args) {
         super({ htsget: true });
         this.baseUrl = args.baseUrl;
         this.trackId = args.trackId;
     }
     async *streamRecordsForRange(chr, min, max, opts) {
-        var _a;
         const base = `${this.baseUrl}/${this.trackId}`;
         const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
-        const chrId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[chr];
+        const chrId = this.chrToIndex?.[chr];
         if (chrId === undefined) {
             yield [];
         }
@@ -77,11 +79,17 @@ export default class HtsgetFile extends BamFile {
             ], chrId, min, max, opts);
         }
     }
+    // @ts-expect-error
     async _readChunk({ chunk }) {
         if (!chunk.buffer) {
             throw new Error('expected chunk.buffer in htsget');
         }
-        return { data: chunk.buffer, cpositions: [], dpositions: [], chunk };
+        return {
+            data: chunk.buffer,
+            cpositions: [],
+            dpositions: [],
+            chunk,
+        };
     }
     async getHeader(opts = {}) {
         const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
@@ -91,11 +99,13 @@ export default class HtsgetFile extends BamFile {
         }
         const data = await result.json();
         const uncba = await concat(data.htsget.urls, opts);
-        if (uncba.readInt32LE(0) !== BAM_MAGIC) {
+        const dataView = new DataView(uncba.buffer);
+        if (dataView.getInt32(0, true) !== BAM_MAGIC) {
             throw new Error('Not a BAM file');
         }
-        const headLen = uncba.readInt32LE(4);
-        const headerText = uncba.toString('utf8', 8, 8 + headLen);
+        const headLen = dataView.getInt32(4, true);
+        const decoder = new TextDecoder('utf8');
+        const headerText = decoder.decode(uncba.subarray(8, 8 + headLen));
         const samHeader = parseHeaderText(headerText);
         // use the @SQ lines in the header to figure out the
         // mapping between ref ref ID numbers and names

package/esm/htsget.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/indexFile.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import { GenericFilehandle } from 'generic-filehandle';
+import { GenericFilehandle } from 'generic-filehandle2';
 import Chunk from './chunk';
 import { BaseOpts } from './util';
 export default abstract class IndexFile {

package/esm/indexFile.js CHANGED Viewed

@@ -1,4 +1,6 @@
 export default class IndexFile {
+    filehandle;
+    renameRefSeq;
     /**
      * @param {filehandle} filehandle
      * @param {function} [renameRefSeqs]

package/esm/indexFile.js.map CHANGED Viewed

	@@ -1 +1 @@
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