@gmod/bam 4.0.1 → 5.0.0

package/CHANGELOG.md

@@ -1,19 +1,15 @@
-## [4.0.1](https://github.com/GMOD/bam-js/compare/v4.0.0...v4.0.1) (2024-11-12)
-
+# [5.0.0](https://github.com/GMOD/bam-js/compare/v4.0.1...v5.0.0) (2024-12-12)
 
 
-# [4.0.0](https://github.com/GMOD/bam-js/compare/v3.0.3...v4.0.0) (2024-11-12)
 
+## [4.0.1](https://github.com/GMOD/bam-js/compare/v4.0.0...v4.0.1) (2024-11-12)
 
+# [4.0.0](https://github.com/GMOD/bam-js/compare/v3.0.3...v4.0.0) (2024-11-12)
 
 ## [3.0.3](https://github.com/GMOD/bam-js/compare/v3.0.0...v3.0.3) (2024-11-11)
 
-
-
 ## [3.0.2](https://github.com/GMOD/bam-js/compare/v3.0.0...v3.0.2) (2024-11-11)
 
-
-
 - republish v3.0.1 since it got tagged on a deleted branch
 
 ## [3.0.1](https://github.com/GMOD/bam-js/compare/v3.0.0...v3.0.1) (2024-11-11)

package/README.md

@@ -26,10 +26,10 @@ var records = await t.getRecordsForRange('ctgA', 0, 50000)
 ```
 
 The `bamPath` argument only works on nodejs. In the browser, you should pass
-`bamFilehandle` with a generic-filehandle e.g. `RemoteFile`
+`bamFilehandle` with a generic-filehandle2 e.g. `RemoteFile`
 
 ```typescript
-const { RemoteFile } = require('generic-filehandle')
+const { RemoteFile } = require('generic-filehandle2')
 const bam = new BamFile({
   bamFilehandle: new RemoteFile('yourfile.bam'), // or a full http url
   baiFilehandle: new RemoteFile('yourfile.bam.bai'), // or a full http url
@@ -76,9 +76,10 @@ The BAM class constructor accepts arguments
   yielding
 
 Note: filehandles implement the Filehandle interface from
-https://www.npmjs.com/package/generic-filehandle. This module offers the path
-and url arguments as convenience methods for supplying the LocalFile and
-RemoteFile
+https://www.npmjs.com/package/generic-filehandle2.
+
+This module offers the path and url arguments as convenience methods for
+supplying the LocalFile and RemoteFile
 
 ### async getRecordsForRange(refName, start, end, opts)
 
@@ -112,7 +113,7 @@ for await (const chunk of file.streamRecordsForRange(
 The `getRecordsForRange` simply wraps this process by concatenating chunks into
 an array
 
-### async getHeader(opts: {....anything to pass to generic-filehandle opts})
+### async getHeader(opts: {....anything to pass to generic-filehandle2 opts})
 
 This obtains the header from `HtsgetFile` or `BamFile`. Retrieves BAM file and
 BAI/CSI header if applicable, or API request for refnames from htsget
@@ -157,11 +158,6 @@ feature.flags // flags
 feature.template_length // TLEN
 ```
 
-#### Note
-
-The reason that we hide the data behind this ".get" function is that we lazily
-decode records on demand, which can reduce memory consumption.
-
 ## License
 
 MIT © [Colin Diesh](https://github.com/cmdcolin)

package/dist/bai.d.ts

@@ -5,7 +5,7 @@ import IndexFile from './indexFile';
 export default class BAI extends IndexFile {
     setupP?: ReturnType<BAI['_parse']>;
     lineCount(refId: number, opts?: BaseOpts): Promise<number>;
-    _parse(opts?: BaseOpts): Promise<{
+    _parse(_opts?: BaseOpts): Promise<{
         bai: boolean;
         firstDataLine: VirtualOffset | undefined;
         maxBlockSize: number;

package/dist/bai.js

@@ -1,13 +1,4 @@
 "use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -35,181 +26,172 @@ function reg2bins(beg, end) {
     ];
 }
 class BAI extends indexFile_1.default {
-    lineCount(refId, opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
-            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;
-        });
+    setupP;
+    async lineCount(refId, opts) {
+        const indexData = await this.parse(opts);
+        return indexData.indices[refId]?.stats?.lineCount || 0;
     }
     // fetch and parse the index
-    _parse(opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const bytes = (yield this.filehandle.readFile(opts));
-            // check BAI magic numbers
-            if (bytes.readUInt32LE(0) !== BAI_MAGIC) {
-                throw new Error('Not a BAI file');
-            }
-            const refCount = bytes.readInt32LE(4);
-            const depth = 5;
-            const binLimit = ((1 << ((depth + 1) * 3)) - 1) / 7;
-            // read the indexes for each reference sequence
-            let curr = 8;
-            let firstDataLine;
-            const indices = new Array(refCount);
-            for (let i = 0; i < refCount; i++) {
-                // the binning index
-                const binCount = bytes.readInt32LE(curr);
-                let stats;
+    async _parse(_opts) {
+        const bytes = await this.filehandle.readFile();
+        const dataView = new DataView(bytes.buffer);
+        // check BAI magic numbers
+        if (dataView.getUint32(0, true) !== BAI_MAGIC) {
+            throw new Error('Not a BAI file');
+        }
+        const refCount = dataView.getInt32(4, true);
+        const depth = 5;
+        const binLimit = ((1 << ((depth + 1) * 3)) - 1) / 7;
+        // read the indexes for each reference sequence
+        let curr = 8;
+        let firstDataLine;
+        const indices = new Array(refCount);
+        for (let i = 0; i < refCount; i++) {
+            // the binning index
+            const binCount = dataView.getInt32(curr, true);
+            let stats;
+            curr += 4;
+            const binIndex = {};
+            for (let j = 0; j < binCount; j += 1) {
+                const bin = dataView.getUint32(curr, true);
                 curr += 4;
-                const binIndex = {};
-                for (let j = 0; j < binCount; j += 1) {
-                    const bin = bytes.readUInt32LE(curr);
+                if (bin === binLimit + 1) {
                     curr += 4;
-                    if (bin === binLimit + 1) {
-                        curr += 4;
-                        stats = (0, util_1.parsePseudoBin)(bytes, curr + 16);
-                        curr += 32;
-                    }
-                    else if (bin > binLimit + 1) {
-                        throw new Error('bai index contains too many bins, please use CSI');
-                    }
-                    else {
-                        const chunkCount = bytes.readInt32LE(curr);
-                        curr += 4;
-                        const chunks = new Array(chunkCount);
-                        for (let k = 0; k < chunkCount; k++) {
-                            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;
-                    }
+                    stats = (0, util_1.parsePseudoBin)(bytes, curr + 16);
+                    curr += 32;
                 }
-                const linearCount = bytes.readInt32LE(curr);
-                curr += 4;
-                // as we're going through the linear index, figure out the smallest
-                // virtual offset in the indexes, which tells us where the BAM header
-                // ends
-                const linearIndex = new Array(linearCount);
-                for (let j = 0; j < linearCount; j++) {
-                    const offset = (0, virtualOffset_1.fromBytes)(bytes, curr);
-                    curr += 8;
-                    firstDataLine = (0, util_1.findFirstData)(firstDataLine, offset);
-                    linearIndex[j] = offset;
+                else if (bin > binLimit + 1) {
+                    throw new Error('bai index contains too many bins, please use CSI');
+                }
+                else {
+                    const chunkCount = dataView.getInt32(curr, true);
+                    curr += 4;
+                    const chunks = new Array(chunkCount);
+                    for (let k = 0; k < chunkCount; k++) {
+                        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;
                 }
-                indices[i] = { binIndex, linearIndex, stats };
-            }
-            return {
-                bai: true,
-                firstDataLine,
-                maxBlockSize: 1 << 16,
-                indices,
-                refCount,
-            };
-        });
-    }
-    indexCov(seqId_1, start_1, end_1) {
-        return __awaiter(this, arguments, void 0, function* (seqId, start, end, opts = {}) {
-            const v = 16384;
-            const range = start !== undefined;
-            const indexData = yield this.parse(opts);
-            const seqIdx = indexData.indices[seqId];
-            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-            if (!seqIdx) {
-                return [];
-            }
-            const { linearIndex = [], stats } = seqIdx;
-            if (linearIndex.length === 0) {
-                return [];
-            }
-            const e = end === undefined ? (linearIndex.length - 1) * v : roundUp(end, v);
-            const s = start === undefined ? 0 : roundDown(start, v);
-            const depths = range
-                ? new Array((e - s) / v)
-                : new Array(linearIndex.length - 1);
-            const totalSize = linearIndex[linearIndex.length - 1].blockPosition;
-            if (e > (linearIndex.length - 1) * v) {
-                throw new Error('query outside of range of linear index');
             }
-            let currentPos = linearIndex[s / v].blockPosition;
-            for (let i = s / v, j = 0; i < e / v; i++, j++) {
-                depths[j] = {
-                    score: linearIndex[i + 1].blockPosition - currentPos,
-                    start: i * v,
-                    end: i * v + v,
-                };
-                currentPos = linearIndex[i + 1].blockPosition;
+            const linearCount = dataView.getInt32(curr, true);
+            curr += 4;
+            // as we're going through the linear index, figure out the smallest
+            // virtual offset in the indexes, which tells us where the BAM header
+            // ends
+            const linearIndex = new Array(linearCount);
+            for (let j = 0; j < linearCount; j++) {
+                const offset = (0, virtualOffset_1.fromBytes)(bytes, curr);
+                curr += 8;
+                firstDataLine = (0, util_1.findFirstData)(firstDataLine, offset);
+                linearIndex[j] = offset;
             }
-            return depths.map(d => (Object.assign(Object.assign({}, d), { score: (d.score * ((stats === null || stats === void 0 ? void 0 : stats.lineCount) || 0)) / totalSize })));
-        });
+            indices[i] = { binIndex, linearIndex, stats };
+        }
+        return {
+            bai: true,
+            firstDataLine,
+            maxBlockSize: 1 << 16,
+            indices,
+            refCount,
+        };
     }
-    blocksForRange(refId_1, min_1, max_1) {
-        return __awaiter(this, arguments, void 0, function* (refId, min, max, opts = {}) {
-            if (min < 0) {
-                min = 0;
-            }
-            const indexData = yield this.parse(opts);
-            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-            if (!indexData) {
-                return [];
-            }
-            const ba = indexData.indices[refId];
-            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-            if (!ba) {
-                return [];
-            }
-            // List of bin #s that overlap min, max
-            const overlappingBins = reg2bins(min, max);
-            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++) {
-                    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-                    if (ba.binIndex[bin]) {
-                        const binChunks = ba.binIndex[bin];
-                        for (const binChunk of binChunks) {
-                            chunks.push(new chunk_1.default(binChunk.minv, binChunk.maxv, bin));
-                        }
+    async indexCov(seqId, start, end, opts = {}) {
+        const v = 16384;
+        const range = start !== undefined;
+        const indexData = await this.parse(opts);
+        const seqIdx = indexData.indices[seqId];
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        if (!seqIdx) {
+            return [];
+        }
+        const { linearIndex = [], stats } = seqIdx;
+        if (linearIndex.length === 0) {
+            return [];
+        }
+        const e = end === undefined ? (linearIndex.length - 1) * v : roundUp(end, v);
+        const s = start === undefined ? 0 : roundDown(start, v);
+        const depths = range
+            ? new Array((e - s) / v)
+            : new Array(linearIndex.length - 1);
+        const totalSize = linearIndex[linearIndex.length - 1].blockPosition;
+        if (e > (linearIndex.length - 1) * v) {
+            throw new Error('query outside of range of linear index');
+        }
+        let currentPos = linearIndex[s / v].blockPosition;
+        for (let i = s / v, j = 0; i < e / v; i++, j++) {
+            depths[j] = {
+                score: linearIndex[i + 1].blockPosition - currentPos,
+                start: i * v,
+                end: i * v + v,
+            };
+            currentPos = linearIndex[i + 1].blockPosition;
+        }
+        return depths.map(d => ({
+            ...d,
+            score: (d.score * (stats?.lineCount || 0)) / totalSize,
+        }));
+    }
+    async blocksForRange(refId, min, max, opts = {}) {
+        if (min < 0) {
+            min = 0;
+        }
+        const indexData = await this.parse(opts);
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        if (!indexData) {
+            return [];
+        }
+        const ba = indexData.indices[refId];
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        if (!ba) {
+            return [];
+        }
+        // List of bin #s that overlap min, max
+        const overlappingBins = reg2bins(min, max);
+        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++) {
+                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                if (ba.binIndex[bin]) {
+                    const binChunks = ba.binIndex[bin];
+                    for (const binChunk of binChunks) {
+                        chunks.push(new chunk_1.default(binChunk.minv, binChunk.maxv, bin));
                     }
                 }
             }
-            // Use the linear index to find minimum file position of chunks that could
-            // contain alignments in the region
-            const nintv = ba.linearIndex.length;
-            let lowest;
-            const minLin = Math.min(min >> 14, nintv - 1);
-            const maxLin = Math.min(max >> 14, nintv - 1);
-            for (let i = minLin; i <= maxLin; ++i) {
-                const vp = ba.linearIndex[i];
-                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-                if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
-                    lowest = vp;
-                }
+        }
+        // Use the linear index to find minimum file position of chunks that could
+        // contain alignments in the region
+        const nintv = ba.linearIndex.length;
+        let lowest;
+        const minLin = Math.min(min >> 14, nintv - 1);
+        const maxLin = Math.min(max >> 14, nintv - 1);
+        for (let i = minLin; i <= maxLin; ++i) {
+            const vp = ba.linearIndex[i];
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+            if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
+                lowest = vp;
             }
-            return (0, util_1.optimizeChunks)(chunks, lowest);
-        });
+        }
+        return (0, util_1.optimizeChunks)(chunks, lowest);
     }
-    parse() {
-        return __awaiter(this, arguments, void 0, function* (opts = {}) {
-            if (!this.setupP) {
-                this.setupP = this._parse(opts).catch((e) => {
-                    this.setupP = undefined;
-                    throw e;
-                });
-            }
-            return this.setupP;
-        });
+    async parse(opts = {}) {
+        if (!this.setupP) {
+            this.setupP = this._parse(opts).catch((e) => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
     }
-    hasRefSeq(seqId_1) {
-        return __awaiter(this, arguments, void 0, function* (seqId, opts = {}) {
-            var _a;
-            const header = yield this.parse(opts);
-            return !!((_a = header.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
-        });
+    async hasRefSeq(seqId, opts = {}) {
+        const header = await this.parse(opts);
+        return !!header.indices[seqId]?.binIndex;
     }
 }
 exports.default = BAI;

package/dist/bai.js.map

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

@@ -1,5 +1,4 @@
-import { Buffer } from 'buffer';
-import { GenericFilehandle } from 'generic-filehandle';
+import { GenericFilehandle } from 'generic-filehandle2';
 import BAI from './bai';
 import CSI from './csi';
 import Chunk from './chunk';
@@ -60,17 +59,17 @@ export default class BamFile {
     streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
     _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
     fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts): Promise<BAMFeature[]>;
-    _readRegion(position: number, size: number, opts?: BaseOpts): Promise<Buffer>;
+    _readRegion(position: number, size: number, opts?: BaseOpts): Promise<Uint8Array<ArrayBuffer>>;
     _readChunk({ chunk, opts }: {
         chunk: Chunk;
         opts: BaseOpts;
     }): Promise<{
-        data: Buffer;
+        data: Uint8Array<ArrayBuffer>;
         cpositions: number[];
         dpositions: number[];
         chunk: Chunk;
     }>;
-    readBamFeatures(ba: Buffer, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
+    readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
     hasRefSeq(seqName: string): Promise<boolean | undefined>;
     lineCount(seqName: string): Promise<number>;
     indexCov(seqName: string, start?: number, end?: number): Promise<{