@gmod/bam 1.1.18 → 2.0.0

package/esm/bai.d.ts

@@ -1,26 +1,45 @@
-/// <reference types="node" />
+import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
-import IndexFile from './indexFile';
 import { BaseOpts } from './util';
+import IndexFile from './indexFile';
 export default class BAI extends IndexFile {
-    baiP?: Promise<Buffer>;
-    parsePseudoBin(bytes: Buffer, offset: number): {
-        lineCount: number;
-    };
-    lineCount(refId: number, opts?: BaseOpts): Promise<any>;
-    fetchBai(opts?: BaseOpts): Promise<Buffer>;
-    _parse(): Promise<{
-        [key: string]: any;
+    setupP?: ReturnType<BAI['_parse']>;
+    lineCount(refId: number, opts?: BaseOpts): Promise<number>;
+    _parse(opts?: BaseOpts): Promise<{
+        bai: boolean;
+        firstDataLine: VirtualOffset | undefined;
+        maxBlockSize: number;
+        indices: {
+            binIndex: {
+                [key: string]: Chunk[];
+            };
+            linearIndex: VirtualOffset[];
+            stats?: {
+                lineCount: number;
+            } | undefined;
+        }[];
+        refCount: number;
     }>;
     indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<{
         start: number;
         end: number;
         score: number;
     }[]>;
-    /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     * @returns {Array[number]}
-     */
-    reg2bins(beg: number, end: number): number[][];
     blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
+    parse(opts?: BaseOpts): Promise<{
+        bai: boolean;
+        firstDataLine: VirtualOffset | undefined;
+        maxBlockSize: number;
+        indices: {
+            binIndex: {
+                [key: string]: Chunk[];
+            };
+            linearIndex: VirtualOffset[];
+            stats?: {
+                lineCount: number;
+            } | undefined;
+        }[];
+        refCount: number;
+    }>;
+    hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
 }

package/esm/bai.js

@@ -1,8 +1,7 @@
-import Long from 'long';
 import { fromBytes } from './virtualOffset';
 import Chunk from './chunk';
+import { optimizeChunks, parsePseudoBin, findFirstData } from './util';
 import IndexFile from './indexFile';
-import { longToNumber, optimizeChunks } from './util';
 const BAI_MAGIC = 21578050; // BAI\1
 function roundDown(n, multiple) {
     return n - (n % multiple);
@@ -10,88 +9,90 @@ function roundDown(n, multiple) {
 function roundUp(n, multiple) {
     return n - (n % multiple) + multiple;
 }
+function reg2bins(beg, end) {
+    end -= 1;
+    return [
+        [0, 0],
+        [1 + (beg >> 26), 1 + (end >> 26)],
+        [9 + (beg >> 23), 9 + (end >> 23)],
+        [73 + (beg >> 20), 73 + (end >> 20)],
+        [585 + (beg >> 17), 585 + (end >> 17)],
+        [4681 + (beg >> 14), 4681 + (end >> 14)],
+    ];
+}
 export default class BAI extends IndexFile {
-    parsePseudoBin(bytes, offset) {
-        const lineCount = longToNumber(Long.fromBytesLE(Array.prototype.slice.call(bytes, offset + 16, offset + 24), true));
-        return { lineCount };
-    }
-    async lineCount(refId, opts = {}) {
-        const prom = await this.parse(opts);
-        const index = prom.indices[refId];
-        if (!index) {
-            return -1;
-        }
-        const ret = index.stats || {};
-        return ret.lineCount === undefined ? -1 : ret.lineCount;
-    }
-    fetchBai(opts = {}) {
-        if (!this.baiP) {
-            this.baiP = this.filehandle.readFile(opts).catch(e => {
-                this.baiP = undefined;
-                throw e;
-            });
-        }
-        return this.baiP;
+    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;
     }
     // fetch and parse the index
-    async _parse() {
-        const data = { bai: true, maxBlockSize: 1 << 16 };
-        const bytes = await this.fetchBai();
+    async _parse(opts) {
+        const bytes = (await this.filehandle.readFile(opts));
         // check BAI magic numbers
         if (bytes.readUInt32LE(0) !== BAI_MAGIC) {
             throw new Error('Not a BAI file');
         }
-        data.refCount = bytes.readInt32LE(4);
+        const refCount = bytes.readInt32LE(4);
         const depth = 5;
         const binLimit = ((1 << ((depth + 1) * 3)) - 1) / 7;
         // read the indexes for each reference sequence
-        data.indices = new Array(data.refCount);
-        let currOffset = 8;
-        for (let i = 0; i < data.refCount; i += 1) {
+        let curr = 8;
+        let firstDataLine;
+        const indices = new Array(refCount);
+        for (let i = 0; i < refCount; i++) {
             // the binning index
-            const binCount = bytes.readInt32LE(currOffset);
+            const binCount = bytes.readInt32LE(curr);
             let stats;
-            currOffset += 4;
+            curr += 4;
             const binIndex = {};
             for (let j = 0; j < binCount; j += 1) {
-                const bin = bytes.readUInt32LE(currOffset);
-                currOffset += 4;
+                const bin = bytes.readUInt32LE(curr);
+                curr += 4;
                 if (bin === binLimit + 1) {
-                    currOffset += 4;
-                    stats = this.parsePseudoBin(bytes, currOffset);
-                    currOffset += 32;
+                    curr += 4;
+                    stats = 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(currOffset);
-                    currOffset += 4;
+                    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);
+                    for (let k = 0; k < chunkCount; k++) {
+                        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;
                 }
             }
-            const linearCount = bytes.readInt32LE(currOffset);
-            currOffset += 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 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 k = 0; k < linearCount; k += 1) {
-                linearIndex[k] = fromBytes(bytes, currOffset);
-                currOffset += 8;
-                this._findFirstData(data, linearIndex[k]);
+            for (let j = 0; j < linearCount; j++) {
+                const offset = fromBytes(bytes, curr);
+                curr += 8;
+                firstDataLine = findFirstData(firstDataLine, offset);
+                linearIndex[j] = offset;
             }
-            data.indices[i] = { binIndex, linearIndex, stats };
+            indices[i] = { binIndex, linearIndex, stats };
         }
-        return data;
+        return {
+            bai: true,
+            firstDataLine,
+            maxBlockSize: 1 << 16,
+            indices,
+            refCount,
+        };
     }
     async indexCov(seqId, start, end, opts = {}) {
         const v = 16384;
@@ -102,18 +103,14 @@ export default class BAI extends IndexFile {
             return [];
         }
         const { linearIndex = [], stats } = seqIdx;
-        if (!linearIndex.length) {
+        if (linearIndex.length === 0) {
             return [];
         }
-        const e = end !== undefined ? roundUp(end, v) : (linearIndex.length - 1) * v;
-        const s = start !== undefined ? roundDown(start, v) : 0;
-        let depths;
-        if (range) {
-            depths = new Array((e - s) / v);
-        }
-        else {
-            depths = new Array(linearIndex.length - 1);
-        }
+        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');
@@ -127,24 +124,10 @@ export default class BAI extends IndexFile {
             };
             currentPos = linearIndex[i + 1].blockPosition;
         }
-        return depths.map(d => {
-            return { ...d, score: (d.score * stats.lineCount) / totalSize };
-        });
-    }
-    /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     * @returns {Array[number]}
-     */
-    reg2bins(beg, end) {
-        end -= 1;
-        return [
-            [0, 0],
-            [1 + (beg >> 26), 1 + (end >> 26)],
-            [9 + (beg >> 23), 9 + (end >> 23)],
-            [73 + (beg >> 20), 73 + (end >> 20)],
-            [585 + (beg >> 17), 585 + (end >> 17)],
-            [4681 + (beg >> 14), 4681 + (end >> 14)],
-        ];
+        return depths.map(d => ({
+            ...d,
+            score: (d.score * ((stats === null || stats === void 0 ? void 0 : stats.lineCount) || 0)) / totalSize,
+        }));
     }
     async blocksForRange(refId, min, max, opts = {}) {
         if (min < 0) {
@@ -159,15 +142,15 @@ export default class BAI extends IndexFile {
             return [];
         }
         // List of bin #s that overlap min, max
-        const overlappingBins = this.reg2bins(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++) {
                 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 binChunk of binChunks) {
+                        chunks.push(binChunk);
                     }
                 }
             }
@@ -175,18 +158,30 @@ export default class BAI extends IndexFile {
         // 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 = null;
+        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];
-            if (vp) {
-                if (!lowest || vp.compareTo(lowest) < 0) {
-                    lowest = vp;
-                }
+            if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
+                lowest = vp;
             }
         }
         return optimizeChunks(chunks, lowest);
     }
+    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=bai.js.map

package/esm/bai.js.map

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package/esm/bamFile.d.ts

@@ -1,28 +1,27 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 import { GenericFilehandle } from 'generic-filehandle';
+import BAI from './bai';
+import CSI from './csi';
 import Chunk from './chunk';
 import BAMFeature from './record';
 import { BamOpts, BaseOpts } from './util';
 export declare const BAM_MAGIC = 21840194;
 export default class BamFile {
-    private renameRefSeq;
-    private bam;
-    private index;
-    private chunkSizeLimit;
-    private fetchSizeLimit;
-    private header;
-    protected chrToIndex: any;
-    protected indexToChr: any;
-    private yieldThreadTime;
+    renameRefSeq: (a: string) => string;
+    bam: GenericFilehandle;
+    header?: string;
+    chrToIndex?: Record<string, number>;
+    indexToChr?: {
+        refName: string;
+        length: number;
+    }[];
+    yieldThreadTime: number;
+    index?: BAI | CSI;
+    htsget: boolean;
+    headerP?: ReturnType<BamFile['getHeaderPre']>;
     private featureCache;
-    /**
-     * @param {object} args
-     * @param {string} [args.bamPath]
-     * @param {FileHandle} [args.bamFilehandle]
-     * @param {string} [args.baiPath]
-     * @param {FileHandle} [args.baiFilehandle]
-     */
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, fetchSizeLimit, chunkSizeLimit, yieldThreadTime, renameRefSeqs, }: {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime, renameRefSeqs, }: {
         bamFilehandle?: GenericFilehandle;
         bamPath?: string;
         bamUrl?: string;
@@ -32,19 +31,25 @@ export default class BamFile {
         csiPath?: string;
         csiFilehandle?: GenericFilehandle;
         csiUrl?: string;
-        fetchSizeLimit?: number;
-        chunkSizeLimit?: number;
         renameRefSeqs?: (a: string) => string;
         yieldThreadTime?: number;
+        htsget?: boolean;
     });
-    getHeader(origOpts?: AbortSignal | BaseOpts): Promise<{
+    getHeaderPre(origOpts?: BaseOpts): Promise<{
         tag: string;
         data: {
             tag: string;
             value: string;
         }[];
-    }[]>;
-    getHeaderText(opts?: BaseOpts): Promise<any>;
+    }[] | undefined>;
+    getHeader(opts?: BaseOpts): Promise<{
+        tag: string;
+        data: {
+            tag: string;
+            value: string;
+        }[];
+    }[] | undefined>;
+    getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
     _readRefSeqs(start: number, refSeqBytes: number, opts?: BaseOpts): Promise<{
         chrToIndex: {
             [key: string]: number;
@@ -56,19 +61,20 @@ export default class BamFile {
     }>;
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<BAMFeature[]>;
     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>;
+    _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>;
     _readChunk({ chunk, opts }: {
         chunk: Chunk;
         opts: BaseOpts;
     }): Promise<{
-        data: any;
-        cpositions: any;
-        dpositions: any;
+        data: Buffer;
+        cpositions: number[];
+        dpositions: number[];
         chunk: Chunk;
     }>;
     readBamFeatures(ba: Buffer, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
-    hasRefSeq(seqName: string): Promise<boolean>;
+    hasRefSeq(seqName: string): Promise<boolean | undefined>;
     lineCount(seqName: string): Promise<number>;
     indexCov(seqName: string, start?: number, end?: number): Promise<{
         start: number;