@gmod/bam 5.0.5 → 5.0.6

package/CHANGELOG.md

@@ -1,27 +1,19 @@
-## [5.0.5](https://github.com/GMOD/bam-js/compare/v5.0.4...v5.0.5) (2024-12-18)
-
+## [5.0.6](https://github.com/GMOD/bam-js/compare/v5.0.5...v5.0.6) (2025-02-28)
 
 
-## [5.0.4](https://github.com/GMOD/bam-js/compare/v5.0.2...v5.0.4) (2024-12-18)
 
+## [5.0.5](https://github.com/GMOD/bam-js/compare/v5.0.4...v5.0.5) (2024-12-18)
 
+## [5.0.4](https://github.com/GMOD/bam-js/compare/v5.0.2...v5.0.4) (2024-12-18)
 
 ## [5.0.3](https://github.com/GMOD/bam-js/compare/v5.0.2...v5.0.3) (2024-12-18)
 
-
-
 ## [5.0.2](https://github.com/GMOD/bam-js/compare/v5.0.1...v5.0.2) (2024-12-17)
 
-
-
 ## [5.0.1](https://github.com/GMOD/bam-js/compare/v5.0.0...v5.0.1) (2024-12-12)
 
-
-
 # [5.0.0](https://github.com/GMOD/bam-js/compare/v4.0.1...v5.0.0) (2024-12-12)
 
-
-
 ## [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)

package/dist/bai.d.ts

@@ -1,7 +1,12 @@
-import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
-import { BaseOpts } from './util';
 import IndexFile from './indexFile';
+import { BaseOpts } from './util';
+import { VirtualOffset } from './virtualOffset';
+export interface IndexCovEntry {
+    start: number;
+    end: number;
+    score: number;
+}
 export default class BAI extends IndexFile {
     setupP?: ReturnType<BAI['_parse']>;
     lineCount(refId: number, opts?: BaseOpts): Promise<number>;
@@ -9,32 +14,28 @@ export default class BAI extends IndexFile {
         bai: boolean;
         firstDataLine: VirtualOffset | undefined;
         maxBlockSize: number;
-        indices: {
-            binIndex: Record<string, Chunk[]>;
+        indices: (refId: number) => {
+            binIndex: Record<number, Chunk[]>;
             linearIndex: VirtualOffset[];
-            stats?: {
+            stats: {
                 lineCount: number;
-            };
-        }[];
+            } | undefined;
+        } | undefined;
         refCount: number;
     }>;
-    indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<{
-        start: number;
-        end: number;
-        score: number;
-    }[]>;
+    indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<IndexCovEntry[]>;
     blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
     parse(opts?: BaseOpts): Promise<{
         bai: boolean;
         firstDataLine: VirtualOffset | undefined;
         maxBlockSize: number;
-        indices: {
-            binIndex: Record<string, Chunk[]>;
+        indices: (refId: number) => {
+            binIndex: Record<number, Chunk[]>;
             linearIndex: VirtualOffset[];
-            stats?: {
+            stats: {
                 lineCount: number;
             } | undefined;
-        }[];
+        } | undefined;
         refCount: number;
     }>;
     hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;

package/dist/bai.js

@@ -3,10 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const virtualOffset_1 = require("./virtualOffset");
+const quick_lru_1 = __importDefault(require("quick-lru"));
 const chunk_1 = __importDefault(require("./chunk"));
-const util_1 = require("./util");
 const indexFile_1 = __importDefault(require("./indexFile"));
+const util_1 = require("./util");
+const virtualOffset_1 = require("./virtualOffset");
 const BAI_MAGIC = 21578050; // BAI\1
 function roundDown(n, multiple) {
     return n - (n % multiple);
@@ -29,9 +30,8 @@ class BAI extends indexFile_1.default {
     setupP;
     async lineCount(refId, opts) {
         const indexData = await this.parse(opts);
-        return indexData.indices[refId]?.stats?.lineCount || 0;
+        return indexData.indices(refId)?.stats?.lineCount || 0;
     }
-    // fetch and parse the index
     async _parse(_opts) {
         const bytes = await this.filehandle.readFile();
         const dataView = new DataView(bytes.buffer);
@@ -45,9 +45,51 @@ class BAI extends indexFile_1.default {
         // read the indexes for each reference sequence
         let curr = 8;
         let firstDataLine;
-        const indices = new Array(refCount);
+        const offsets = [];
         for (let i = 0; i < refCount; i++) {
-            // the binning index
+            offsets.push(curr);
+            const binCount = dataView.getInt32(curr, true);
+            curr += 4;
+            for (let j = 0; j < binCount; j += 1) {
+                const bin = dataView.getUint32(curr, true);
+                curr += 4;
+                if (bin === binLimit + 1) {
+                    curr += 4;
+                    curr += 32;
+                }
+                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;
+                    for (let k = 0; k < chunkCount; k++) {
+                        curr += 8;
+                        curr += 8;
+                    }
+                }
+            }
+            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;
+            }
+        }
+        const indicesCache = new quick_lru_1.default({
+            maxSize: 5,
+        });
+        function getIndices(refId) {
+            let curr = offsets[refId];
+            if (curr === undefined) {
+                return undefined;
+            }
             const binCount = dataView.getInt32(curr, true);
             let stats;
             curr += 4;
@@ -90,22 +132,34 @@ class BAI extends indexFile_1.default {
                 firstDataLine = (0, util_1.findFirstData)(firstDataLine, offset);
                 linearIndex[j] = offset;
             }
-            indices[i] = { binIndex, linearIndex, stats };
+            return {
+                binIndex,
+                linearIndex,
+                stats,
+            };
         }
         return {
             bai: true,
             firstDataLine,
             maxBlockSize: 1 << 16,
-            indices,
+            indices: (refId) => {
+                if (!indicesCache.has(refId)) {
+                    const result = getIndices(refId);
+                    if (result) {
+                        indicesCache.set(refId, result);
+                    }
+                    return result;
+                }
+                return indicesCache.get(refId);
+            },
             refCount,
         };
     }
-    async indexCov(seqId, start, end, opts = {}) {
+    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
+        const seqIdx = indexData.indices(seqId);
         if (!seqIdx) {
             return [];
         }
@@ -145,8 +199,7 @@ class BAI extends indexFile_1.default {
         if (!indexData) {
             return [];
         }
-        const ba = indexData.indices[refId];
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        const ba = indexData.indices(refId);
         if (!ba) {
             return [];
         }
@@ -156,7 +209,6 @@ class BAI extends indexFile_1.default {
         // 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) {
@@ -173,7 +225,6 @@ class BAI extends indexFile_1.default {
         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;
             }
@@ -191,7 +242,7 @@ class BAI extends indexFile_1.default {
     }
     async hasRefSeq(seqId, opts = {}) {
         const header = await this.parse(opts);
-        return !!header.indices[seqId]?.binIndex;
+        return !!header.indices(seqId)?.binIndex;
     }
 }
 exports.default = BAI;

package/dist/bai.js.map

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package/dist/bamFile.d.ts

@@ -1,9 +1,9 @@
-import { GenericFilehandle } from 'generic-filehandle2';
 import BAI from './bai';
-import CSI from './csi';
 import Chunk from './chunk';
+import CSI from './csi';
 import BAMFeature from './record';
 import { BamOpts, BaseOpts } from './util';
+import type { GenericFilehandle } from 'generic-filehandle2';
 export declare const BAM_MAGIC = 21840194;
 export default class BamFile {
     renameRefSeq: (a: string) => string;
@@ -59,7 +59,6 @@ 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<Uint8Array<ArrayBuffer>>;
     _readChunk({ chunk, opts }: {
         chunk: Chunk;
         opts: BaseOpts;
@@ -72,10 +71,6 @@ export default class BamFile {
     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<{
-        start: number;
-        end: number;
-        score: number;
-    }[]>;
+    indexCov(seqName: string, start?: number, end?: number): Promise<import("./bai").IndexCovEntry[]>;
     blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
 }

package/dist/bamFile.js

@@ -4,40 +4,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BAM_MAGIC = void 0;
-const crc32_1 = __importDefault(require("crc/calculators/crc32"));
+const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const crc32_1 = __importDefault(require("crc/calculators/crc32"));
 const generic_filehandle2_1 = require("generic-filehandle2");
-const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
-// locals
 const bai_1 = __importDefault(require("./bai"));
 const csi_1 = __importDefault(require("./csi"));
+const nullFilehandle_1 = __importDefault(require("./nullFilehandle"));
 const record_1 = __importDefault(require("./record"));
 const sam_1 = require("./sam");
 const util_1 = require("./util");
 exports.BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
-async function gen2array(gen) {
-    let out = [];
-    for await (const x of gen) {
-        out = out.concat(x);
-    }
-    return out;
-}
-class NullFilehandle {
-    read() {
-        throw new Error('never called');
-    }
-    stat() {
-        throw new Error('never called');
-    }
-    readFile() {
-        throw new Error('never called');
-    }
-    close() {
-        throw new Error('never called');
-    }
-}
 class BamFile {
     renameRefSeq;
     bam;
@@ -74,7 +53,7 @@ class BamFile {
         }
         else if (htsget) {
             this.htsget = true;
-            this.bam = new NullFilehandle();
+            this.bam = new nullFilehandle_1.default();
         }
         else {
             throw new Error('unable to initialize bam');
@@ -184,7 +163,7 @@ class BamFile {
         return { chrToIndex, indexToChr };
     }
     async getRecordsForRange(chr, min, max, opts) {
-        return gen2array(this.streamRecordsForRange(chr, min, max, opts));
+        return (0, util_1.gen2array)(this.streamRecordsForRange(chr, min, max, opts));
     }
     async *streamRecordsForRange(chr, min, max, opts) {
         await this.getHeader(opts);
@@ -288,12 +267,9 @@ class BamFile {
         }));
         return mateFeatPromises.flat();
     }
-    async _readRegion(position, size, opts = {}) {
-        return this.bam.read(size, position, opts);
-    }
     async _readChunk({ chunk, opts }) {
-        const buffer = await this._readRegion(chunk.minv.blockPosition, chunk.fetchedSize(), opts);
-        const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buffer, chunk);
+        const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, opts);
+        const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk);
         return { data, cpositions, dpositions, chunk };
     }
     async readBamFeatures(ba, cpositions, dpositions, chunk) {

package/dist/bamFile.js.map

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

@@ -1,11 +1,11 @@
-import VirtualOffset from './virtualOffset';
+import { Offset } from './virtualOffset';
 export default class Chunk {
-    minv: VirtualOffset;
-    maxv: VirtualOffset;
+    minv: Offset;
+    maxv: Offset;
     bin: number;
     _fetchedSize?: number | undefined;
     buffer?: Uint8Array;
-    constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, _fetchedSize?: number | undefined);
+    constructor(minv: Offset, maxv: Offset, bin: number, _fetchedSize?: number | undefined);
     toUniqueString(): string;
     toString(): string;
     compareTo(b: Chunk): number;

package/dist/chunk.js.map

@@ -1 +1 @@
-{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,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;AAlCD,wBAkCC"}
+{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAIf;IACA;IACA;IACA;IANF,MAAM,CAAa;IAE1B,YACS,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAQ;QACZ,SAAI,GAAJ,IAAI,CAAQ;QACZ,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;AAlCD,wBAkCC"}

package/dist/csi.d.ts

@@ -1,7 +1,7 @@
-import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
-import { BaseOpts } from './util';
 import IndexFile from './indexFile';
+import { BaseOpts } from './util';
+import { VirtualOffset } from './virtualOffset';
 export default class CSI extends IndexFile {
     private maxBinNumber;
     private depth;
@@ -42,12 +42,12 @@ export default class CSI extends IndexFile {
         formatFlags?: number | undefined;
         csiVersion: number;
         firstDataLine: VirtualOffset | undefined;
-        indices: {
+        indices: (refId: number) => {
             binIndex: Record<string, Chunk[]>;
-            stats?: {
+            stats: {
                 lineCount: number;
-            };
-        }[];
+            } | undefined;
+        } | undefined;
         refCount: number;
         csi: boolean;
         maxBlockSize: number;
@@ -74,12 +74,12 @@ export default class CSI extends IndexFile {
         formatFlags?: number | undefined;
         csiVersion: number;
         firstDataLine: VirtualOffset | undefined;
-        indices: {
+        indices: (refId: number) => {
             binIndex: Record<string, Chunk[]>;
-            stats?: {
+            stats: {
                 lineCount: number;
             } | undefined;
-        }[];
+        } | undefined;
         refCount: number;
         csi: boolean;
         maxBlockSize: number;