@gmod/bam 5.0.4 → 5.0.6

package/esm/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/esm/bai.js

@@ -1,7 +1,8 @@
-import { fromBytes } from './virtualOffset';
+import QuickLRU from 'quick-lru';
 import Chunk from './chunk';
-import { optimizeChunks, parsePseudoBin, findFirstData } from './util';
 import IndexFile from './indexFile';
+import { findFirstData, optimizeChunks, parsePseudoBin } from './util';
+import { fromBytes } from './virtualOffset';
 const BAI_MAGIC = 21578050; // BAI\1
 function roundDown(n, multiple) {
     return n - (n % multiple);
@@ -24,9 +25,8 @@ export default class BAI extends IndexFile {
     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);
@@ -40,9 +40,51 @@ export default class BAI extends IndexFile {
         // 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 = fromBytes(bytes, curr);
+                curr += 8;
+                firstDataLine = findFirstData(firstDataLine, offset);
+                linearIndex[j] = offset;
+            }
+        }
+        const indicesCache = new QuickLRU({
+            maxSize: 5,
+        });
+        function getIndices(refId) {
+            let curr = offsets[refId];
+            if (curr === undefined) {
+                return undefined;
+            }
             const binCount = dataView.getInt32(curr, true);
             let stats;
             curr += 4;
@@ -85,22 +127,34 @@ export default class BAI extends IndexFile {
                 firstDataLine = 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 [];
         }
@@ -140,8 +194,7 @@ export default class BAI extends IndexFile {
         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 [];
         }
@@ -151,7 +204,6 @@ export default class BAI extends IndexFile {
         // 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) {
@@ -168,7 +220,6 @@ export default class BAI extends IndexFile {
         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;
             }
@@ -186,7 +237,7 @@ export default class BAI extends IndexFile {
     }
     async hasRefSeq(seqId, opts = {}) {
         const header = await this.parse(opts);
-        return !!header.indices[seqId]?.binIndex;
+        return !!header.indices(seqId)?.binIndex;
     }
 }
 //# sourceMappingURL=bai.js.map

package/esm/bai.js.map

@@ -1 +1 @@
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package/esm/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/esm/bamFile.js

@@ -1,37 +1,16 @@
-import crc32 from 'crc/calculators/crc32';
+import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
+import crc32 from 'crc/calculators/crc32';
 import { LocalFile, RemoteFile } from 'generic-filehandle2';
-import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import QuickLRU from 'quick-lru';
-// locals
 import BAI from './bai';
 import CSI from './csi';
+import NullFilehandle from './nullFilehandle';
 import BAMFeature from './record';
 import { parseHeaderText } from './sam';
-import { checkAbortSignal, timeout, makeOpts } from './util';
+import { checkAbortSignal, gen2array, makeOpts, timeout, } from './util';
 export const 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');
-    }
-}
 export default class BamFile {
     renameRefSeq;
     bam;
@@ -282,12 +261,9 @@ export default 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 unzipChunkSlice(buffer, chunk);
+        const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, opts);
+        const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk);
         return { data, cpositions, dpositions, chunk };
     }
     async readBamFeatures(ba, cpositions, dpositions, chunk) {

package/esm/bamFile.js.map

@@ -1 +1 @@
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package/esm/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/esm/chunk.js.map

@@ -1 +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"}
+{"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,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"}

package/esm/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;

package/esm/csi.js

@@ -1,8 +1,9 @@
 import { unzip } from '@gmod/bgzf-filehandle';
-import VirtualOffset, { fromBytes } from './virtualOffset';
+import QuickLRU from 'quick-lru';
 import Chunk from './chunk';
-import { optimizeChunks, findFirstData, parsePseudoBin, parseNameBytes, } from './util';
 import IndexFile from './indexFile';
+import { findFirstData, optimizeChunks, parseNameBytes, parsePseudoBin, } from './util';
+import { VirtualOffset, fromBytes } from './virtualOffset';
 const CSI1_MAGIC = 21582659; // CSI\1
 const CSI2_MAGIC = 38359875; // CSI\2
 function lshift(num, bits) {
@@ -18,7 +19,7 @@ export default class CSI extends IndexFile {
     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;
     }
     async indexCov() {
         return [];
@@ -71,14 +72,43 @@ export default class CSI extends IndexFile {
         this.minShift = dataView.getInt32(4, true);
         this.depth = dataView.getInt32(8, true);
         this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
+        const maxBinNumber = this.maxBinNumber;
         const auxLength = dataView.getInt32(12, true);
         const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined;
         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);
+        const offsets = [];
         for (let i = 0; i < refCount; i++) {
+            offsets.push(curr);
+            const binCount = dataView.getInt32(curr, true);
+            curr += 4;
+            for (let j = 0; j < binCount; j++) {
+                const bin = dataView.getUint32(curr, true);
+                curr += 4;
+                if (bin > this.maxBinNumber) {
+                    curr += 28 + 16;
+                }
+                else {
+                    curr += 8;
+                    const chunkCount = dataView.getInt32(curr, true);
+                    curr += 4;
+                    for (let k = 0; k < chunkCount; k += 1) {
+                        curr += 8;
+                        curr += 8;
+                    }
+                }
+            }
+        }
+        const indicesCache = new QuickLRU({
+            maxSize: 5,
+        });
+        function getIndices(refId) {
+            let curr = offsets[refId];
+            if (curr === undefined) {
+                return undefined;
+            }
             // the binning index
             const binCount = dataView.getInt32(curr, true);
             curr += 4;
@@ -87,7 +117,7 @@ export default class CSI extends IndexFile {
             for (let j = 0; j < binCount; j++) {
                 const bin = dataView.getUint32(curr, true);
                 curr += 4;
-                if (bin > this.maxBinNumber) {
+                if (bin > maxBinNumber) {
                     stats = parsePseudoBin(bytes, curr + 28);
                     curr += 28 + 16;
                 }
@@ -108,12 +138,24 @@ export default class CSI extends IndexFile {
                     binIndex[bin] = chunks;
                 }
             }
-            indices[i] = { binIndex, stats };
+            return {
+                binIndex,
+                stats,
+            };
         }
         return {
             csiVersion,
             firstDataLine,
-            indices,
+            indices: (refId) => {
+                if (!indicesCache.has(refId)) {
+                    const result = getIndices(refId);
+                    if (result) {
+                        indicesCache.set(refId, result);
+                    }
+                    return result;
+                }
+                return indicesCache.get(refId);
+            },
             refCount,
             csi: true,
             maxBlockSize: 1 << 16,
@@ -125,8 +167,7 @@ export default class CSI extends IndexFile {
             min = 0;
         }
         const indexData = await this.parse(opts);
-        const ba = indexData.indices[refId];
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        const ba = indexData.indices(refId);
         if (!ba) {
             return [];
         }
@@ -138,7 +179,6 @@ export default class CSI extends IndexFile {
         // 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 c of binChunks) {
@@ -187,7 +227,7 @@ export default class CSI extends IndexFile {
     }
     async hasRefSeq(seqId, opts = {}) {
         const header = await this.parse(opts);
-        return !!header.indices[seqId]?.binIndex;
+        return !!header.indices(seqId)?.binIndex;
     }
 }
 //# sourceMappingURL=csi.js.map

package/esm/csi.js.map

@@ -1 +1 @@
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