@gmod/bam 7.3.4 → 7.5.0
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.
- package/README.md +11 -29
- package/dist/bai.js +10 -7
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +26 -9
- package/dist/bamFile.js +95 -47
- package/dist/bamFile.js.map +1 -1
- package/dist/csi.js +2 -2
- package/dist/csi.js.map +1 -1
- package/dist/htsget.js +2 -2
- package/dist/htsget.js.map +1 -1
- package/dist/index.d.ts +1 -2
- package/dist/index.js +2 -1
- package/dist/index.js.map +1 -1
- package/dist/record.d.ts +2 -1
- package/dist/record.js +150 -39
- package/dist/record.js.map +1 -1
- package/dist/util.d.ts +0 -18
- package/dist/util.js +5 -36
- package/dist/util.js.map +1 -1
- package/esm/bai.js +10 -7
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +26 -9
- package/esm/bamFile.js +95 -47
- package/esm/bamFile.js.map +1 -1
- package/esm/csi.js +2 -2
- package/esm/csi.js.map +1 -1
- package/esm/htsget.js +2 -2
- package/esm/htsget.js.map +1 -1
- package/esm/index.d.ts +1 -2
- package/esm/index.js +1 -1
- package/esm/index.js.map +1 -1
- package/esm/record.d.ts +2 -1
- package/esm/record.js +150 -39
- package/esm/record.js.map +1 -1
- package/esm/util.d.ts +0 -18
- package/esm/util.js +5 -32
- package/esm/util.js.map +1 -1
- package/package.json +3 -1
- package/src/bai.ts +15 -8
- package/src/bamFile.ts +121 -57
- package/src/csi.ts +10 -2
- package/src/htsget.ts +6 -2
- package/src/index.ts +1 -2
- package/src/record.ts +163 -46
- package/src/util.ts +13 -63
package/esm/bamFile.d.ts
CHANGED
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@@ -1,4 +1,3 @@
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1
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-
import QuickLRU from '@jbrowse/quick-lru';
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2
1
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import BAI from './bai.ts';
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3
2
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import CSI from './csi.ts';
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4
3
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import BAMFeature from './record.ts';
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@@ -24,10 +23,23 @@ export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
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}) => T;
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export declare const BAM_MAGIC = 21840194;
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interface ChunkEntry<T> {
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-
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-
maxBlock: number;
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+
bytes: number;
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features: T[];
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}
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+
export declare const DEFAULT_MAX_CACHE_BYTES: number;
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declare class ChunkFeatureCache<T> {
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maxBytes: number;
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private entries;
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private bytes;
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constructor(maxBytes: number);
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get size(): number;
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get byteSize(): number;
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get(key: string): ChunkEntry<T> | undefined;
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set(key: string, entry: ChunkEntry<T>): void;
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delete(key: string): void;
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clear(): void;
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[Symbol.iterator](): MapIterator<[string, ChunkEntry<T>]>;
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}
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export default class BamFile<T extends BamRecordLike = BAMFeature> {
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renameRefSeq: (a: string) => string;
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bam: GenericFilehandle;
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@@ -40,9 +52,9 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
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index?: BAI | CSI;
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htsget: boolean;
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headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
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-
chunkFeatureCache:
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chunkFeatureCache: ChunkFeatureCache<T>;
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private RecordClass;
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-
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, }: {
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+
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, }: {
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bamFilehandle?: GenericFilehandle;
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bamPath?: string;
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bamUrl?: string;
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@@ -55,6 +67,8 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
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renameRefSeqs?: (a: string) => string;
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htsget?: boolean;
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recordClass?: BamRecordClass<T>;
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/** budget for the parsed-chunk cache, in decompressed bytes */
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maxCacheBytes?: number;
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});
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getHeaderPre(opts?: BaseOpts): Promise<{
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tag: string;
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@@ -73,11 +87,14 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
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getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
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private getSeqId;
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getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
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-
private
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private
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private _cachedChunkFeatures;
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private _fetchChunkFeatures;
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fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
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-
_readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<
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-
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_readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<{
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features: T[];
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bytes: number;
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}>;
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readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): T[];
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hasRefSeq(seqName: string, opts?: BaseOpts): Promise<boolean>;
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lineCount(seqName: string, opts?: BaseOpts): Promise<number>;
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indexCov(seqName: string, start?: number, end?: number): Promise<never[] | import("./bai.ts").IndexCovEntry[]>;
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package/esm/bamFile.js
CHANGED
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@@ -1,5 +1,4 @@
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1
1
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import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
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-
import QuickLRU from '@jbrowse/quick-lru';
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2
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import crc32 from 'crc/calculators/crc32';
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3
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import { LocalFile, RemoteFile } from 'generic-filehandle2';
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4
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import BAI from "./bai.js";
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@@ -7,16 +6,73 @@ import CSI from "./csi.js";
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6
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import NullFilehandle from "./nullFilehandle.js";
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7
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import BAMFeature from "./record.js";
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8
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import { parseHeaderText } from "./sam.js";
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-
import { appendInRange,
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9
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+
import { appendInRange, parseRefSeqs } from "./util.js";
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10
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export const BAM_MAGIC = 21840194;
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const blockLen = 1 << 16;
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function resolveFilehandle(filehandle, path, url) {
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return (filehandle ??
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(path ? new LocalFile(path) : url ? new RemoteFile(url) : undefined));
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}
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-
function chunkCacheKey(chunk
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function chunkCacheKey(chunk) {
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const { minv, maxv } = chunk;
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-
return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}
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return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
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}
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// Every record in an entry is a view into its chunk's decompressed buffer, so
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// caching one entry pins that whole buffer — 8MB apiece on the nanopore and
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// 2kb-read test files, and optimizeChunks merges spans up to 5MB *compressed*,
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// so tens of MB is possible. A count-based LRU therefore gives no bound on
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// memory at all, which is why this budgets by decompressed bytes instead. It is
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// the *only* bound: a query keeps every chunk it parsed, since a chunk dropped
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// here costs a re-download and re-decompress the next time the view moves.
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export const DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024;
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class ChunkFeatureCache {
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maxBytes;
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entries = new Map();
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bytes = 0;
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constructor(maxBytes) {
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this.maxBytes = maxBytes;
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}
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get size() {
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return this.entries.size;
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}
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get byteSize() {
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return this.bytes;
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}
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get(key) {
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const entry = this.entries.get(key);
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if (entry) {
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// re-insert so Map iteration order stays least-recently-used first
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this.entries.delete(key);
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this.entries.set(key, entry);
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}
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return entry;
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}
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set(key, entry) {
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this.delete(key);
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this.entries.set(key, entry);
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this.bytes += entry.bytes;
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// Evict from the least-recently-used end. The size > 1 guard means a single
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// chunk larger than the whole budget is still kept: the caller needs it for
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// the query in flight, and dropping it would only force a re-decompress.
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const lru = this.entries.keys();
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while (this.bytes > this.maxBytes && this.entries.size > 1) {
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this.delete(lru.next().value);
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}
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}
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delete(key) {
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const entry = this.entries.get(key);
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if (entry) {
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this.entries.delete(key);
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this.bytes -= entry.bytes;
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}
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}
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clear() {
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this.entries.clear();
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this.bytes = 0;
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}
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[Symbol.iterator]() {
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return this.entries[Symbol.iterator]();
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}
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}
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export default class BamFile {
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renameRefSeq;
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@@ -27,15 +83,13 @@ export default class BamFile {
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index;
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htsget = false;
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headerP;
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// Cache for parsed features by chunk
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chunkFeatureCache = new QuickLRU({
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maxSize: 100,
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});
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// Cache for parsed features by chunk, bounded by decompressed bytes
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chunkFeatureCache;
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RecordClass;
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constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, }) {
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constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = DEFAULT_MAX_CACHE_BYTES, }) {
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this.renameRefSeq = renameRefSeqs;
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this.RecordClass = (recordClass ?? BAMFeature);
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this.chunkFeatureCache = new ChunkFeatureCache(maxCacheBytes);
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const bamFh = resolveFilehandle(bamFilehandle, bamPath, bamUrl);
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if (bamFh) {
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this.bam = bamFh;
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@@ -75,7 +129,7 @@ export default class BamFile {
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? await this.bam.readFile()
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: await this.bam.read(readLen, 0);
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let uncba = await unzip(buffer);
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const dataView = new DataView(uncba.buffer);
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const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
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133
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if (dataView.getInt32(0, true) !== BAM_MAGIC) {
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throw new Error('Not a BAM file');
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}
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@@ -123,18 +177,23 @@ export default class BamFile {
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return [];
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}
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const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
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-
return this.
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return this._fetchChunkFeatures(chunks, chrId, min, max, opts);
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}
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//
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// Parsed records for a chunk, reading and decompressing it only on a miss.
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// Every path that wants a chunk's features goes through here — mate lookups
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// included, since a viewAsPairs query revisits the same mate chunks each time
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// the view moves.
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async _cachedChunkFeatures(chunk, opts) {
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const cacheKey = chunkCacheKey(chunk);
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let entry = this.chunkFeatureCache.get(cacheKey);
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if (!entry) {
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entry = await this._readChunkFeatures(chunk, opts);
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this.chunkFeatureCache.set(cacheKey, entry);
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}
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return entry.features;
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}
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async
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const { viewAsPairs,
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async _fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
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const { viewAsPairs, onProgress } = opts;
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const result = [];
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let totalBytes = 0;
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for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
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@@ -144,27 +203,10 @@ export default class BamFile {
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onProgress?.(0, totalBytes);
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for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
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const chunk = chunks[ci];
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const
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const minBlock = chunk.minv.blockPosition;
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const maxBlock = chunk.maxv.blockPosition;
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let records;
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const cached = this.chunkFeatureCache.get(cacheKey);
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if (cached) {
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records = cached.features;
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}
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else {
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this.evictOverlappingChunks(minBlock, maxBlock);
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const allRecords = await this._readChunkFeatures(chunk, opts);
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records = filterBy ? applyFilters(allRecords, filterBy) : allRecords;
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this.chunkFeatureCache.set(cacheKey, {
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minBlock,
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maxBlock,
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features: records,
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});
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}
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const features = await this._cachedChunkFeatures(chunk, opts);
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downloadedBytes += chunk.fetchedSize();
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onProgress?.(downloadedBytes, totalBytes);
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appendInRange(
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appendInRange(features, chrId, min, max, result);
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}
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if (viewAsPairs) {
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const pairs = await this.fetchPairs(chrId, result, opts);
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@@ -176,12 +218,15 @@ export default class BamFile {
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}
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async fetchPairs(chrId, records, opts) {
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const { pairAcrossChr, maxInsertSize = 200000 } = opts;
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-
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+
// Map, not a plain object: read names come from the file, and on a plain
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// object a read named "constructor" would read back Object.prototype's and
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// make the count NaN.
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const readNameCounts = new Map();
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const readIds = new Set();
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for (let i = 0, l = records.length; i < l; i++) {
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const r = records[i];
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const name = r.name;
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-
readNameCounts
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readNameCounts.set(name, (readNameCounts.get(name) ?? 0) + 1);
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readIds.add(r.fileOffset);
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}
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const matePromises = [];
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@@ -189,7 +234,7 @@ export default class BamFile {
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189
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const f = records[i];
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const name = f.name;
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if (this.index &&
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-
readNameCounts
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237
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+
readNameCounts.get(name) === 1 &&
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193
238
|
(pairAcrossChr ||
|
|
194
239
|
(f.next_refid === chrId &&
|
|
195
240
|
Math.abs(f.start - f.next_pos) < maxInsertSize))) {
|
|
@@ -206,11 +251,11 @@ export default class BamFile {
|
|
|
206
251
|
}
|
|
207
252
|
}
|
|
208
253
|
const mateFeatLists = await Promise.all([...map.values()].map(async (c) => {
|
|
209
|
-
const features = await this.
|
|
254
|
+
const features = await this._cachedChunkFeatures(c, opts);
|
|
210
255
|
const mateRecs = [];
|
|
211
256
|
for (let i = 0, l = features.length; i < l; i++) {
|
|
212
257
|
const feature = features[i];
|
|
213
|
-
if (readNameCounts
|
|
258
|
+
if (readNameCounts.get(feature.name) === 1 &&
|
|
214
259
|
!readIds.has(feature.fileOffset)) {
|
|
215
260
|
mateRecs.push(feature);
|
|
216
261
|
}
|
|
@@ -229,13 +274,16 @@ export default class BamFile {
|
|
|
229
274
|
signal: opts.signal,
|
|
230
275
|
});
|
|
231
276
|
const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk);
|
|
232
|
-
return
|
|
277
|
+
return {
|
|
278
|
+
features: this.readBamFeatures(data, cpositions, dpositions, chunk),
|
|
279
|
+
bytes: data.byteLength,
|
|
280
|
+
};
|
|
233
281
|
}
|
|
234
|
-
|
|
282
|
+
readBamFeatures(ba, cpositions, dpositions, chunk) {
|
|
235
283
|
let blockStart = 0;
|
|
236
284
|
const sink = [];
|
|
237
285
|
let pos = 0;
|
|
238
|
-
const dataView = new DataView(ba.buffer);
|
|
286
|
+
const dataView = new DataView(ba.buffer, ba.byteOffset, ba.byteLength);
|
|
239
287
|
const hasDpositions = dpositions.length > 0;
|
|
240
288
|
const hasCpositions = cpositions.length > 0;
|
|
241
289
|
while (blockStart + 4 < ba.length) {
|
package/esm/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
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+
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|
package/esm/csi.js
CHANGED
|
@@ -22,7 +22,7 @@ export default class CSI extends IndexFile {
|
|
|
22
22
|
return [];
|
|
23
23
|
}
|
|
24
24
|
parseAuxData(bytes, offset) {
|
|
25
|
-
const dataView = new DataView(bytes.buffer);
|
|
25
|
+
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
|
|
26
26
|
const formatFlags = dataView.getUint32(offset, true);
|
|
27
27
|
const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
|
|
28
28
|
const format = ['generic', 'SAM', 'VCF'][formatFlags & 0xf];
|
|
@@ -53,7 +53,7 @@ export default class CSI extends IndexFile {
|
|
|
53
53
|
async _parse(opts) {
|
|
54
54
|
const buffer = await this.filehandle.readFile(opts);
|
|
55
55
|
const bytes = await unzip(buffer);
|
|
56
|
-
const dataView = new DataView(bytes.buffer);
|
|
56
|
+
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
|
|
57
57
|
let csiVersion;
|
|
58
58
|
const magic = dataView.getUint32(0, true);
|
|
59
59
|
if (magic === CSI1_MAGIC) {
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,EAAE,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAC1D,OAAO,EACL,cAAc,EACd,aAAa,EACb,cAAc,EACd,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,WAAW,GAAG,IAAI,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAE3C,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;IAEpB,uEAAuE;IACvE,iEAAiE;IACjE,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,
|
|
1
|
+
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|
package/esm/htsget.js
CHANGED
|
@@ -47,7 +47,7 @@ export default class HtsgetFile extends BamFile {
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|
47
47
|
signal: opts?.signal,
|
|
48
48
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});
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|
49
49
|
const zero = new VirtualOffset(0, 0);
|
|
50
|
-
const allRecords =
|
|
50
|
+
const allRecords = this.readBamFeatures(uncba, [], [], new Chunk(zero, zero, 0));
|
|
51
51
|
return appendInRange(allRecords, chrId, min, max);
|
|
52
52
|
}
|
|
53
53
|
async getHeaderPre(opts = {}) {
|
|
@@ -57,7 +57,7 @@ export default class HtsgetFile extends BamFile {
|
|
|
57
57
|
const uncba = await fetchAndConcat(data.htsget.urls, {
|
|
58
58
|
signal: opts.signal,
|
|
59
59
|
});
|
|
60
|
-
const dataView = new DataView(uncba.buffer);
|
|
60
|
+
const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
|
|
61
61
|
if (dataView.getInt32(0, true) !== BAM_MAGIC) {
|
|
62
62
|
throw new Error('Not a BAM file');
|
|
63
63
|
}
|
package/esm/htsget.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,OAAO,EAAE,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,EAAE,eAAe,EAAE,MAAM,UAAU,CAAA;AAC1C,OAAO,EAAE,aAAa,EAAE,gBAAgB,EAAE,MAAM,WAAW,CAAA;AAC3D,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAWlD,KAAK,UAAU,OAAO,CAAC,GAAW,EAAE,IAAkB;IACpD,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAClC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC,CAAA;IAC5E,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,KAAK,UAAU,UAAU,CAAC,EAAE,GAAG,EAAE,OAAO,EAAe,EAAE,IAAkB;IACzE,0EAA0E;IAC1E,uDAAuD;IACvD,+CAA+C;IAC/C,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,IAAI,EAAE,CAAA;IACpD,MAAM,GAAG,GAAG,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC;QACjC,CAAC,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC;QACpB,CAAC,CAAC,MAAM,OAAO,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAClD,OAAO,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;AAChD,CAAC;AAED,KAAK,UAAU,cAAc,CAAC,GAAkB,EAAE,IAAkB;IAClE,2EAA2E;IAC3E,OAAO,gBAAgB,CACrB,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,CAAC,EAAC,EAAE,CAAC,KAAK,CAAC,MAAM,UAAU,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CACxE,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAEnB,SAAQ,OAAU;IACV,OAAO,CAAQ;IAEf,OAAO,CAAQ;IAEvB,YAAY,IAIX;QACC,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,CAAC,WAAW,EAAE,CAAC,CAAA;QACtD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;QAEd,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;QAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;QAC7E,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACvC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;YAC5D,MAAM,EAAE,IAAI,EAAE,MAAM;SACrB,CAAC,CAAA;QAEF,MAAM,IAAI,GAAG,IAAI,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACpC,MAAM,UAAU,GAAG,IAAI,CAAC,eAAe,CACrC,KAAK,EACL,EAAE,EACF,EAAE,EACF,IAAI,KAAK,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CACzB,CAAA;QAED,OAAO,aAAa,CAAC,UAAU,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;IACnD,CAAC;IAED,KAAK,CAAC,YAAY,CAAC,OAAiB,EAAE;QACpC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;QAC3E,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACvC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE;YACnD,MAAM,EAAE,IAAI,CAAC,MAAM;SACpB,CAAC,CAAA;QACF,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QAED,IAAI,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC7C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QACD,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAE1C,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;QACjC,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAC,CAAA;QACjE,MAAM,SAAS,GAAG,eAAe,CAAC,UAAU,CAAC,CAAA;QAE7C,oDAAoD;QACpD,+CAA+C;QAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;QAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;QACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;YAChD,IAAI,OAAO,GAAG,EAAE,CAAA;YAChB,IAAI,MAAM,GAAG,CAAC,CAAA;YACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;gBAC/B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBACtB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;qBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;YACH,CAAC;YACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;QACvC,CAAC;QACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,OAAO,SAAS,CAAA;IAClB,CAAC;CACF"}
|
package/esm/index.d.ts
CHANGED
|
@@ -1,8 +1,7 @@
|
|
|
1
1
|
export { default as BAI } from './bai.ts';
|
|
2
|
-
export { default as BamFile } from './bamFile.ts';
|
|
2
|
+
export { DEFAULT_MAX_CACHE_BYTES, default as BamFile } from './bamFile.ts';
|
|
3
3
|
export { default as CSI } from './csi.ts';
|
|
4
4
|
export { default as BamRecord } from './record.ts';
|
|
5
5
|
export { default as HtsgetFile } from './htsget.ts';
|
|
6
6
|
export type { Bytes } from './record.ts';
|
|
7
|
-
export type { FilterBy, TagFilter } from './util.ts';
|
|
8
7
|
export type { BamRecordClass, BamRecordLike } from './bamFile.ts';
|
package/esm/index.js
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
export { default as BAI } from "./bai.js";
|
|
2
|
-
export { default as BamFile } from "./bamFile.js";
|
|
2
|
+
export { DEFAULT_MAX_CACHE_BYTES, default as BamFile } from "./bamFile.js";
|
|
3
3
|
export { default as CSI } from "./csi.js";
|
|
4
4
|
export { default as BamRecord } from "./record.js";
|
|
5
5
|
export { default as HtsgetFile } from "./htsget.js";
|
package/esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,cAAc,CAAA;
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,uBAAuB,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,cAAc,CAAA;AAC1E,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAClD,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA"}
|
package/esm/record.d.ts
CHANGED
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
export type NumericCigar = Uint32Array | Int32Array | number[];
|
|
1
2
|
export interface Bytes {
|
|
2
3
|
start: number;
|
|
3
4
|
end: number;
|
|
@@ -55,7 +56,7 @@ export default class BamRecord {
|
|
|
55
56
|
private _computeLengthOnRef;
|
|
56
57
|
private _computeNumericCigar;
|
|
57
58
|
get length_on_ref(): number;
|
|
58
|
-
get NUMERIC_CIGAR():
|
|
59
|
+
get NUMERIC_CIGAR(): NumericCigar;
|
|
59
60
|
get CIGAR(): string;
|
|
60
61
|
get num_cigar_ops(): number;
|
|
61
62
|
get num_cigar_bytes(): number;
|