@gmod/bam 7.4.0 → 7.6.0
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/bamFile.d.ts +13 -9
- package/dist/bamFile.js +121 -45
- package/dist/bamFile.js.map +1 -1
- package/dist/index.d.ts +0 -1
- package/dist/record.d.ts +1 -5
- package/dist/record.js +57 -10
- package/dist/record.js.map +1 -1
- package/dist/util.d.ts +0 -18
- package/dist/util.js +0 -30
- package/dist/util.js.map +1 -1
- package/esm/bamFile.d.ts +13 -9
- package/esm/bamFile.js +122 -46
- package/esm/bamFile.js.map +1 -1
- package/esm/index.d.ts +0 -1
- package/esm/record.d.ts +1 -5
- package/esm/record.js +57 -10
- package/esm/record.js.map +1 -1
- package/esm/util.d.ts +0 -18
- package/esm/util.js +0 -27
- package/esm/util.js.map +1 -1
- package/package.json +2 -1
- package/src/bamFile.ts +142 -49
- package/src/index.ts +0 -1
- package/src/record.ts +66 -10
- package/src/util.ts +0 -60
package/dist/util.d.ts
CHANGED
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@@ -1,20 +1,10 @@
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1
1
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import Chunk from './chunk.ts';
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2
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import type { Offset, VirtualOffset } from './virtualOffset.ts';
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-
export interface TagFilter {
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tag: string;
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value?: string;
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}
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export interface FilterBy {
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flagInclude?: number;
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flagExclude?: number;
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tagFilter?: TagFilter;
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-
}
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export interface BamOpts {
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viewAsPairs?: boolean;
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pairAcrossChr?: boolean;
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maxInsertSize?: number;
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signal?: AbortSignal;
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filterBy?: FilterBy;
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/**
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* Called as the BGZF blocks covering the query are fetched, with cumulative
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* downloaded bytes and the total to fetch. Reported at block granularity (one
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@@ -52,14 +42,6 @@ export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (a
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refIdToName: string[];
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};
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export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;
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-
export declare function filterReadFlag(flags: number, flagInclude: number, flagExclude: number): boolean;
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-
export declare function filterTagValue(readVal: unknown, filterVal?: string): boolean;
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interface Filterable {
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flags: number;
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tags: Record<string, unknown>;
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getTag?(tag: string): unknown;
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}
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export declare function applyFilters<T extends Filterable>(records: T[], filterBy: FilterBy): T[];
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interface Positioned {
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ref_id: number;
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start: number;
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package/dist/util.js
CHANGED
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@@ -10,9 +10,6 @@ exports.parseRefSeqs = parseRefSeqs;
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exports.findFirstData = findFirstData;
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exports.parseNameBytes = parseNameBytes;
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exports.concatUint8Array = concatUint8Array;
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-
exports.filterReadFlag = filterReadFlag;
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exports.filterTagValue = filterTagValue;
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exports.applyFilters = applyFilters;
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exports.appendInRange = appendInRange;
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const chunk_ts_1 = __importDefault(require("./chunk.js"));
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const long_ts_1 = require("./long.js");
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@@ -183,33 +180,6 @@ function concatUint8Array(args) {
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}
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return mergedArray;
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}
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-
function filterReadFlag(flags, flagInclude, flagExclude) {
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-
return (flags & flagInclude) !== flagInclude || (flags & flagExclude) !== 0;
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-
}
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-
function filterTagValue(readVal, filterVal) {
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return filterVal === '*'
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? readVal === undefined
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: `${readVal}` !== `${filterVal}`;
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}
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-
// Read a single tag, preferring the targeted accessor. Reaching for `tags`
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// instead would decode every unrelated tag on the record (NM/AS/ms/de/… — often
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-
// ~10 per read) just to test one, which measured 2.6x the cost of getTag.
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function readTag(record, tag) {
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return record.getTag ? record.getTag(tag) : record.tags[tag];
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-
}
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// Apply flagInclude/flagExclude/tagFilter to a list of records.
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function applyFilters(records, filterBy) {
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const { flagInclude = 0, flagExclude = 0, tagFilter } = filterBy;
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const out = [];
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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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if (!filterReadFlag(r.flags, flagInclude, flagExclude) &&
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!(tagFilter && filterTagValue(readTag(r, tagFilter.tag), tagFilter.value))) {
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out.push(r);
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}
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}
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return out;
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-
}
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// Append records overlapping [min, max) on `chrId` into `out` (or a fresh
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// array if omitted). Records are assumed coordinate-sorted (by ref_id, then
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// start), so we stop scanning once we pass `max` within `chrId` or move past
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package/dist/util.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;
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1
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+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;AA+BA,wCAsEC;AAED,wCAIC;AASD,wCA2BC;AAKD,oCAsCC;AAED,sCASC;AAGD,wCAuBC;AAED,4CAYC;AAYD,sCAoBC;AA7QD,0DAA8B;AAC9B,uCAAmD;AA8BnD,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAe;IAC7D,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAA;IACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO,MAAM,CAAA;IACf,CAAC;IAED,0DAA0D;IAC1D,IAAI,QAAiB,CAAA;IACrB,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,WAAW,GAAG,MAAM,CAAC,aAAa,CAAA;QACxC,MAAM,UAAU,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,QAAQ,GAAG,EAAE,CAAA;QACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;YACxB,MAAM,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;YACvB,MAAM,GAAG,GACP,IAAI,CAAC,aAAa,GAAG,WAAW,IAAI,IAAI,CAAC,YAAY,GAAG,UAAU,CAAA;YACpE,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACtB,CAAC;QACH,CAAC;QACD,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC1B,OAAO,QAAQ,CAAA;QACjB,CAAC;IACH,CAAC;SAAM,CAAC;QACN,QAAQ,GAAG,MAAM,CAAA;IACnB,CAAC;IAED,QAAQ,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACvB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,yEAAyE;IACzE,uEAAuE;IACvE,MAAM,YAAY,GAAY,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAA;IAC5C,IAAI,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,CAAC,aAAa,CAAA;IAClD,IAAI,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,CAAC,aAAa,CAAA;IAElD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACzC,MAAM,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,oEAAoE;QACpE,yEAAyE;QACzE,IACE,aAAa,GAAG,YAAY,GAAG,KAAK;YACpC,aAAa,GAAG,YAAY,GAAG,OAAO,EACtC,CAAC;YACD,MAAM,SAAS,GAAG,YAAY,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAE,CAAA;YACxD,MAAM,GAAG,GACP,aAAa,GAAG,YAAY;gBAC5B,KAAK,CAAC,IAAI,CAAC,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,YAAY,CAAA;YACvD,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,YAAY,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,IAAI,kBAAK,CAC/C,SAAS,CAAC,IAAI,EACd,KAAK,CAAC,IAAI,EACV,SAAS,CAAC,GAAG,EACb,KAAK,CAAC,WAAW,CAClB,CAAA;gBACD,YAAY,GAAG,aAAa,CAAA;YAC9B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACxB,YAAY,GAAG,aAAa,CAAA;YAC5B,YAAY,GAAG,aAAa,CAAA;QAC9B,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,SAAgB,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO;QACL,SAAS,EAAE,IAAA,iCAAuB,EAAC,KAAK,EAAE,MAAM,CAAC;KAClD,CAAA;AACH,CAAC;AAED,6EAA6E;AAC7E,kFAAkF;AAClF,kFAAkF;AAClF,iFAAiF;AACjF,kFAAkF;AAClF,iFAAiF;AACjF,yEAAyE;AACzE,SAAgB,cAAc,CAC5B,MAAe,EACf,kBAA4B,EAAE;IAE9B,MAAM,UAAU,GAAG,CAAC,GAAG,eAAe,CAAC,CAAA;IACvC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;IAC7D,CAAC;IACD,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IAEhC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,aAAa,CAAA;QAChC,2CAA2C;QAC3C,IAAI,EAAE,GAAG,CAAC,CAAA;QACV,IAAI,EAAE,GAAG,UAAU,CAAC,MAAM,CAAA;QAC1B,OAAO,EAAE,GAAG,EAAE,EAAE,CAAC;YACf,MAAM,GAAG,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,CAAA;YAC3B,IAAI,UAAU,CAAC,GAAG,CAAE,GAAG,GAAG,EAAE,CAAC;gBAC3B,EAAE,GAAG,GAAG,CAAA;YACV,CAAC;iBAAM,CAAC;gBACN,EAAE,GAAG,GAAG,GAAG,CAAC,CAAA;YACd,CAAC;QACH,CAAC;QACD,IAAI,EAAE,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC;YAC3B,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,UAAU,CAAC,EAAE,CAAE,CAAC,CAAA;QAC1D,CAAC;IACH,CAAC;AACH,CAAC;AAED,6EAA6E;AAC7E,4EAA4E;AAC5E,eAAe;AACf,SAAgB,YAAY,CAC1B,KAAiB,EACjB,KAAa,EACb,YAAmC;IAEnC,IAAI,KAAK,GAAG,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;IACD,MAAM,IAAI,GAAG,QAAQ,CAAC,QAAQ,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;IAC3C,kEAAkE;IAClE,uDAAuD;IACvD,MAAM,UAAU,GAA2B,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;IAC9D,MAAM,UAAU,GAA0C,EAAE,CAAA;IAC5D,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,CAAA;IAEvC,IAAI,CAAC,GAAG,KAAK,GAAG,CAAC,CAAA;IACjB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,CAAC;QAC9B,IAAI,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC;YACzB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACxC,IAAI,CAAC,GAAG,CAAC,GAAG,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC;YACjC,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,OAAO,GAAG,YAAY,CAC1B,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,KAAK,GAAG,CAAC,CAAC,CAAC,CACzD,CAAA;QACD,MAAM,IAAI,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,GAAG,KAAK,GAAG,CAAC,EAAE,IAAI,CAAC,CAAA;QACnD,UAAU,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACvB,UAAU,CAAC,IAAI,CAAC,EAAE,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAA;QAC1C,CAAC,IAAI,CAAC,GAAG,KAAK,CAAA;IAChB,CAAC;IACD,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,CAAA;AACnC,CAAC;AAED,SAAgB,aAAa,CAC3B,aAAwC,EACxC,aAA4B;IAE5B,OAAO,aAAa;QAClB,CAAC,CAAC,aAAa,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;YAC1C,CAAC,CAAC,aAAa;YACf,CAAC,CAAC,aAAa;QACjB,CAAC,CAAC,aAAa,CAAA;AACnB,CAAC;AAED,4FAA4F;AAC5F,SAAgB,cAAc,CAC5B,UAAsB,EACtB,eAAwC,CAAC,CAAC,EAAE,CAAC,CAAC;IAE9C,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;IACjC,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,MAAM,WAAW,GAAa,EAAE,CAAA;IAChC,MAAM,WAAW,GAA2B,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;IAC/D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;gBACtB,MAAM,OAAO,GAAG,YAAY,CAC1B,OAAO,CAAC,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,aAAa,EAAE,CAAC,CAAC,CAAC,CACtD,CAAA;gBACD,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;gBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;YAClC,CAAC;YACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;YACrB,SAAS,EAAE,CAAA;QACb,CAAC;IACH,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AAED,SAAgB,gBAAgB,CAAC,IAAkB;IACjD,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,IAAI,KAAK,CAAC,MAAM,CAAA;IAC7B,CAAC;IACD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;IAC/C,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC9B,MAAM,IAAI,KAAK,CAAC,MAAM,CAAA;IACxB,CAAC;IACD,OAAO,WAAW,CAAA;AACpB,CAAC;AAQD,0EAA0E;AAC1E,4EAA4E;AAC5E,6EAA6E;AAC7E,iDAAiD;AACjD,SAAgB,aAAa,CAC3B,OAAY,EACZ,KAAa,EACb,GAAW,EACX,GAAW,EACX,MAAW,EAAE;IAEb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC/C,MAAM,CAAC,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QACrB,IAAI,CAAC,CAAC,MAAM,KAAK,KAAK,EAAE,CAAC;YACvB,IAAI,CAAC,CAAC,KAAK,IAAI,GAAG,EAAE,CAAC;gBACnB,MAAK;YACP,CAAC;iBAAM,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC;gBACxB,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACb,CAAC;QACH,CAAC;aAAM,IAAI,CAAC,CAAC,MAAM,GAAG,KAAK,EAAE,CAAC;YAC5B,MAAK;QACP,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
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package/esm/bamFile.d.ts
CHANGED
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@@ -2,7 +2,6 @@ import BAI from './bai.ts';
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2
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import CSI from './csi.ts';
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import BAMFeature from './record.ts';
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import type Chunk from './chunk.ts';
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import type { Bytes } from './record.ts';
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import type { BamOpts, BaseOpts } from './util.ts';
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import type { GenericFilehandle } from 'generic-filehandle2';
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export interface BamRecordLike {
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@@ -16,15 +15,9 @@ export interface BamRecordLike {
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flags: number;
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tags: Record<string, unknown>;
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}
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export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (
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bytes: Bytes;
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fileOffset: number;
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dataView: DataView;
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}) => T;
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export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (byteArray: Uint8Array, start: number, end: number, fileOffset: number, dataView: DataView) => T;
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export declare const BAM_MAGIC = 21840194;
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interface ChunkEntry<T> {
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minBlock: number;
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maxBlock: number;
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28
21
|
bytes: number;
|
|
29
22
|
features: T[];
|
|
30
23
|
}
|
|
@@ -55,6 +48,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
55
48
|
htsget: boolean;
|
|
56
49
|
headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
|
|
57
50
|
chunkFeatureCache: ChunkFeatureCache<T>;
|
|
51
|
+
private inFlightChunks;
|
|
58
52
|
private RecordClass;
|
|
59
53
|
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, }: {
|
|
60
54
|
bamFilehandle?: GenericFilehandle;
|
|
@@ -88,8 +82,18 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
88
82
|
}[] | undefined>;
|
|
89
83
|
getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
|
|
90
84
|
private getSeqId;
|
|
85
|
+
/**
|
|
86
|
+
* Records overlapping `chr:min-max`.
|
|
87
|
+
*
|
|
88
|
+
* The returned records are CACHED AND SHARED — two queries resolving to the
|
|
89
|
+
* same chunk span get the same objects back, so treat them as read-only.
|
|
90
|
+
* Anything you want to attach for the duration of one query belongs on a
|
|
91
|
+
* wrapper you own, never on the record; writing a field here silently rebinds
|
|
92
|
+
* it for every other query still holding that read. See ADR 0006.
|
|
93
|
+
*/
|
|
91
94
|
getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
|
|
92
|
-
private
|
|
95
|
+
private _startChunkRead;
|
|
96
|
+
private _cachedChunkFeatures;
|
|
93
97
|
private _fetchChunkFeatures;
|
|
94
98
|
fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
|
|
95
99
|
_readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<{
|
package/esm/bamFile.js
CHANGED
|
@@ -6,17 +6,13 @@ import CSI from "./csi.js";
|
|
|
6
6
|
import NullFilehandle from "./nullFilehandle.js";
|
|
7
7
|
import BAMFeature from "./record.js";
|
|
8
8
|
import { parseHeaderText } from "./sam.js";
|
|
9
|
-
import { appendInRange,
|
|
9
|
+
import { appendInRange, parseRefSeqs } from "./util.js";
|
|
10
10
|
export const BAM_MAGIC = 21840194;
|
|
11
11
|
const blockLen = 1 << 16;
|
|
12
12
|
function resolveFilehandle(filehandle, path, url) {
|
|
13
13
|
return (filehandle ??
|
|
14
14
|
(path ? new LocalFile(path) : url ? new RemoteFile(url) : undefined));
|
|
15
15
|
}
|
|
16
|
-
// Keyed on the chunk's byte span only, not on filterBy: the cached value is the
|
|
17
|
-
// unfiltered parsed records (decompression + parse is the expensive part).
|
|
18
|
-
// Filters are applied cheaply on retrieval so toggling a filter over the same
|
|
19
|
-
// region is a cache hit rather than a re-decompress.
|
|
20
16
|
function chunkCacheKey(chunk) {
|
|
21
17
|
const { minv, maxv } = chunk;
|
|
22
18
|
return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
|
|
@@ -25,8 +21,14 @@ function chunkCacheKey(chunk) {
|
|
|
25
21
|
// caching one entry pins that whole buffer — 8MB apiece on the nanopore and
|
|
26
22
|
// 2kb-read test files, and optimizeChunks merges spans up to 5MB *compressed*,
|
|
27
23
|
// so tens of MB is possible. A count-based LRU therefore gives no bound on
|
|
28
|
-
// memory at all, which is why this budgets by decompressed bytes instead.
|
|
24
|
+
// memory at all, which is why this budgets by decompressed bytes instead. It is
|
|
25
|
+
// the *only* bound: a query keeps every chunk it parsed, since a chunk dropped
|
|
26
|
+
// here costs a re-download and re-decompress the next time the view moves.
|
|
29
27
|
export const DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024;
|
|
28
|
+
// How many of a query's chunks to read at once. Six is the HTTP/1.1
|
|
29
|
+
// per-host connection cap browsers enforce, so going much above it buys
|
|
30
|
+
// nothing on the transport that matters and only widens peak memory.
|
|
31
|
+
const MAX_CONCURRENT_CHUNK_READS = 6;
|
|
30
32
|
class ChunkFeatureCache {
|
|
31
33
|
maxBytes;
|
|
32
34
|
entries = new Map();
|
|
@@ -85,9 +87,12 @@ export default class BamFile {
|
|
|
85
87
|
index;
|
|
86
88
|
htsget = false;
|
|
87
89
|
headerP;
|
|
88
|
-
// Cache for parsed features by chunk
|
|
89
|
-
// When a new chunk overlaps a cached chunk, we evict the cached one
|
|
90
|
+
// Cache for parsed features by chunk, bounded by decompressed bytes
|
|
90
91
|
chunkFeatureCache;
|
|
92
|
+
// Chunks currently being read, so concurrent queries share one decompress
|
|
93
|
+
// instead of racing. Entries live only until the read settles; the resolved
|
|
94
|
+
// features land in chunkFeatureCache.
|
|
95
|
+
inFlightChunks = new Map();
|
|
91
96
|
RecordClass;
|
|
92
97
|
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = DEFAULT_MAX_CACHE_BYTES, }) {
|
|
93
98
|
this.renameRefSeq = renameRefSeqs;
|
|
@@ -174,6 +179,15 @@ export default class BamFile {
|
|
|
174
179
|
await this.getHeader(opts);
|
|
175
180
|
return this.chrToIndex?.[seqName];
|
|
176
181
|
}
|
|
182
|
+
/**
|
|
183
|
+
* Records overlapping `chr:min-max`.
|
|
184
|
+
*
|
|
185
|
+
* The returned records are CACHED AND SHARED — two queries resolving to the
|
|
186
|
+
* same chunk span get the same objects back, so treat them as read-only.
|
|
187
|
+
* Anything you want to attach for the duration of one query belongs on a
|
|
188
|
+
* wrapper you own, never on the record; writing a field here silently rebinds
|
|
189
|
+
* it for every other query still holding that read. See ADR 0006.
|
|
190
|
+
*/
|
|
177
191
|
async getRecordsForRange(chr, min, max, opts) {
|
|
178
192
|
const chrId = await this.getSeqId(chr, opts);
|
|
179
193
|
if (chrId === undefined || !this.index) {
|
|
@@ -182,16 +196,68 @@ export default class BamFile {
|
|
|
182
196
|
const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
|
|
183
197
|
return this._fetchChunkFeatures(chunks, chrId, min, max, opts);
|
|
184
198
|
}
|
|
185
|
-
//
|
|
186
|
-
|
|
187
|
-
|
|
188
|
-
|
|
189
|
-
|
|
199
|
+
// Read a chunk, publish it to the cache, and keep the in-flight promise
|
|
200
|
+
// discoverable while it runs.
|
|
201
|
+
_startChunkRead(cacheKey, chunk, opts) {
|
|
202
|
+
const promise = this._readChunkFeatures(chunk, opts).then(entry => {
|
|
203
|
+
this.chunkFeatureCache.set(cacheKey, entry);
|
|
204
|
+
return entry;
|
|
205
|
+
});
|
|
206
|
+
const inFlight = { promise, signal: opts.signal };
|
|
207
|
+
this.inFlightChunks.set(cacheKey, inFlight);
|
|
208
|
+
// Only clear our own entry: a retry may already have replaced it. `.then(f,
|
|
209
|
+
// f)` rather than `.finally(f)` so the handler's own promise never carries
|
|
210
|
+
// an unhandled rejection.
|
|
211
|
+
const clear = () => {
|
|
212
|
+
if (this.inFlightChunks.get(cacheKey) === inFlight) {
|
|
213
|
+
this.inFlightChunks.delete(cacheKey);
|
|
190
214
|
}
|
|
215
|
+
};
|
|
216
|
+
promise.then(clear, clear);
|
|
217
|
+
return promise;
|
|
218
|
+
}
|
|
219
|
+
// Parsed records for a chunk, reading and decompressing it only on a miss.
|
|
220
|
+
// Every path that wants a chunk's features goes through here — mate lookups
|
|
221
|
+
// included, since a viewAsPairs query revisits the same mate chunks each time
|
|
222
|
+
// the view moves.
|
|
223
|
+
//
|
|
224
|
+
// This hands the SAME record objects to every query that hits the key, which
|
|
225
|
+
// is what makes callers' per-query writes onto a record leak across queries
|
|
226
|
+
// (ADR 0006). Caching the inflated buffer and re-scanning per query would give
|
|
227
|
+
// each caller its own objects, but roughly doubles a warm query on dense data
|
|
228
|
+
// — measured, and rejected, in that ADR.
|
|
229
|
+
async _cachedChunkFeatures(chunk, opts) {
|
|
230
|
+
const cacheKey = chunkCacheKey(chunk);
|
|
231
|
+
const cached = this.chunkFeatureCache.get(cacheKey);
|
|
232
|
+
if (cached) {
|
|
233
|
+
return cached.features;
|
|
234
|
+
}
|
|
235
|
+
// Join a read already running for this chunk rather than decompressing it a
|
|
236
|
+
// second time. jbrowse fetches a row of adjacent blocks concurrently and
|
|
237
|
+
// they collapse onto very few chunk keys, so without this a query pays for
|
|
238
|
+
// the same inflate several times over — the dominant cost of a cold query
|
|
239
|
+
// (ADR 0003).
|
|
240
|
+
const pending = this.inFlightChunks.get(cacheKey);
|
|
241
|
+
if (!pending) {
|
|
242
|
+
return (await this._startChunkRead(cacheKey, chunk, opts)).features;
|
|
243
|
+
}
|
|
244
|
+
try {
|
|
245
|
+
return (await pending.promise).features;
|
|
246
|
+
}
|
|
247
|
+
catch (e) {
|
|
248
|
+
// The read we joined was started by another caller. If that caller
|
|
249
|
+
// aborted and we did not, the failure is theirs and says nothing about
|
|
250
|
+
// our query, so start over — which picks up the cache, joins a sibling's
|
|
251
|
+
// retry, or reads under our own signal. Any other failure (and our own
|
|
252
|
+
// abort) propagates as it would have without sharing.
|
|
253
|
+
if (!pending.signal?.aborted || opts.signal?.aborted) {
|
|
254
|
+
throw e;
|
|
255
|
+
}
|
|
256
|
+
return this._cachedChunkFeatures(chunk, opts);
|
|
191
257
|
}
|
|
192
258
|
}
|
|
193
259
|
async _fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
|
|
194
|
-
const { viewAsPairs,
|
|
260
|
+
const { viewAsPairs, onProgress } = opts;
|
|
195
261
|
const result = [];
|
|
196
262
|
let totalBytes = 0;
|
|
197
263
|
for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
|
|
@@ -199,24 +265,42 @@ export default class BamFile {
|
|
|
199
265
|
}
|
|
200
266
|
let downloadedBytes = 0;
|
|
201
267
|
onProgress?.(0, totalBytes);
|
|
268
|
+
const featureLists = new Array(chunks.length);
|
|
269
|
+
if (chunks.length === 1) {
|
|
270
|
+
// Very common — most small files, and any query landing inside one bin.
|
|
271
|
+
// Worth its own path: the pool below allocates a closure, a worker array
|
|
272
|
+
// and a Promise.all, all of which is pure overhead for one chunk and
|
|
273
|
+
// measurable on queries that take ~0.2ms.
|
|
274
|
+
featureLists[0] = await this._cachedChunkFeatures(chunks[0], opts);
|
|
275
|
+
onProgress?.(totalBytes, totalBytes);
|
|
276
|
+
}
|
|
277
|
+
else {
|
|
278
|
+
// Fetch the chunks concurrently. A query routinely spans a dozen or more
|
|
279
|
+
// chunks (14.8 on average for a 20kb window on the test 18MB file) and
|
|
280
|
+
// each is its own range request, so reading them one after another costs
|
|
281
|
+
// a network round trip apiece — the dominant cost of a remote query, well
|
|
282
|
+
// ahead of decompression. Bounded because browsers cap concurrent
|
|
283
|
+
// connections per host anyway, and an unbounded fan-out would inflate
|
|
284
|
+
// every chunk of a whole-chromosome query at once.
|
|
285
|
+
let next = 0;
|
|
286
|
+
const readNext = async () => {
|
|
287
|
+
while (next < chunks.length) {
|
|
288
|
+
const ci = next++;
|
|
289
|
+
const chunk = chunks[ci];
|
|
290
|
+
featureLists[ci] = await this._cachedChunkFeatures(chunk, opts);
|
|
291
|
+
downloadedBytes += chunk.fetchedSize();
|
|
292
|
+
onProgress?.(downloadedBytes, totalBytes);
|
|
293
|
+
}
|
|
294
|
+
};
|
|
295
|
+
const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length);
|
|
296
|
+
await Promise.all(Array.from({ length: workers }, () => readNext()));
|
|
297
|
+
}
|
|
298
|
+
// Append in chunk order, not completion order, so the result is the same
|
|
299
|
+
// sequence a sequential walk produced. (That is not coordinate order — bins
|
|
300
|
+
// at different levels cover overlapping spans — but it is what every caller
|
|
301
|
+
// has always been handed.)
|
|
202
302
|
for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
|
|
203
|
-
|
|
204
|
-
const cacheKey = chunkCacheKey(chunk);
|
|
205
|
-
const minBlock = chunk.minv.blockPosition;
|
|
206
|
-
const maxBlock = chunk.maxv.blockPosition;
|
|
207
|
-
let cached = this.chunkFeatureCache.get(cacheKey);
|
|
208
|
-
if (!cached) {
|
|
209
|
-
this.evictOverlappingChunks(minBlock, maxBlock);
|
|
210
|
-
const { features, bytes } = await this._readChunkFeatures(chunk, opts);
|
|
211
|
-
cached = { minBlock, maxBlock, bytes, features };
|
|
212
|
-
this.chunkFeatureCache.set(cacheKey, cached);
|
|
213
|
-
}
|
|
214
|
-
const records = filterBy
|
|
215
|
-
? applyFilters(cached.features, filterBy)
|
|
216
|
-
: cached.features;
|
|
217
|
-
downloadedBytes += chunk.fetchedSize();
|
|
218
|
-
onProgress?.(downloadedBytes, totalBytes);
|
|
219
|
-
appendInRange(records, chrId, min, max, result);
|
|
303
|
+
appendInRange(featureLists[ci], chrId, min, max, result);
|
|
220
304
|
}
|
|
221
305
|
if (viewAsPairs) {
|
|
222
306
|
const pairs = await this.fetchPairs(chrId, result, opts);
|
|
@@ -261,7 +345,7 @@ export default class BamFile {
|
|
|
261
345
|
}
|
|
262
346
|
}
|
|
263
347
|
const mateFeatLists = await Promise.all([...map.values()].map(async (c) => {
|
|
264
|
-
const
|
|
348
|
+
const features = await this._cachedChunkFeatures(c, opts);
|
|
265
349
|
const mateRecs = [];
|
|
266
350
|
for (let i = 0, l = features.length; i < l; i++) {
|
|
267
351
|
const feature = features[i];
|
|
@@ -306,20 +390,12 @@ export default class BamFile {
|
|
|
306
390
|
}
|
|
307
391
|
}
|
|
308
392
|
if (blockEnd < ba.length) {
|
|
309
|
-
const feature = new this.RecordClass(
|
|
310
|
-
|
|
311
|
-
|
|
312
|
-
|
|
313
|
-
|
|
314
|
-
|
|
315
|
-
fileOffset: hasCpositions
|
|
316
|
-
? cpositions[pos] * (1 << 8) +
|
|
317
|
-
(blockStart - dpositions[pos]) +
|
|
318
|
-
chunk.minv.dataPosition +
|
|
319
|
-
1
|
|
320
|
-
: crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
|
|
321
|
-
dataView,
|
|
322
|
-
});
|
|
393
|
+
const feature = new this.RecordClass(ba, blockStart, blockEnd, hasCpositions
|
|
394
|
+
? cpositions[pos] * (1 << 8) +
|
|
395
|
+
(blockStart - dpositions[pos]) +
|
|
396
|
+
chunk.minv.dataPosition +
|
|
397
|
+
1
|
|
398
|
+
: crc32(ba.subarray(blockStart, blockEnd)) >>> 0, dataView);
|
|
323
399
|
sink.push(feature);
|
|
324
400
|
}
|
|
325
401
|
blockStart = blockEnd + 1;
|
package/esm/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/esm/index.d.ts
CHANGED
|
@@ -4,5 +4,4 @@ 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/record.d.ts
CHANGED
|
@@ -16,11 +16,7 @@ export default class BamRecord {
|
|
|
16
16
|
private _cachedNumericCigar?;
|
|
17
17
|
private _cachedNUMERIC_MD?;
|
|
18
18
|
private _cachedSeqStart?;
|
|
19
|
-
constructor(
|
|
20
|
-
bytes: Bytes;
|
|
21
|
-
fileOffset: number;
|
|
22
|
-
dataView: DataView;
|
|
23
|
-
});
|
|
19
|
+
constructor(byteArray: Uint8Array, start: number, end: number, fileOffset: number, dataView: DataView);
|
|
24
20
|
get byteArray(): Uint8Array<ArrayBufferLike>;
|
|
25
21
|
get flags(): number;
|
|
26
22
|
get ref_id(): number;
|
package/esm/record.js
CHANGED
|
@@ -42,6 +42,42 @@ const ASCII_CIGAR_CODES = [
|
|
|
42
42
|
77, 73, 68, 78, 83, 72, 80, 61, 88, 63, 63, 63, 63, 63, 63, 63,
|
|
43
43
|
];
|
|
44
44
|
const textDecoder = new TextDecoder();
|
|
45
|
+
// Interned two-char tag names keyed on the packed byte pair. Worth more than
|
|
46
|
+
// the saved String.fromCharCode: the tags object is null-prototype and so in
|
|
47
|
+
// dictionary mode, and handing it a string V8 has already hashed halves the
|
|
48
|
+
// per-tag insert cost.
|
|
49
|
+
const TAG_NAMES = new Map();
|
|
50
|
+
function tagName(b0, b1) {
|
|
51
|
+
const key = (b0 << 8) | b1;
|
|
52
|
+
let name = TAG_NAMES.get(key);
|
|
53
|
+
if (name === undefined) {
|
|
54
|
+
name = String.fromCharCode(b0, b1);
|
|
55
|
+
TAG_NAMES.set(key, name);
|
|
56
|
+
}
|
|
57
|
+
return name;
|
|
58
|
+
}
|
|
59
|
+
// TextDecoder carries ~0.35us of fixed setup per call, which dominates for the
|
|
60
|
+
// short values Z/H tags usually hold (MD, RG, PG, ...): char codes are 4x
|
|
61
|
+
// faster at 8 bytes, 2x at 16, and the two cross over at 32.
|
|
62
|
+
const SHORT_STRING_THRESHOLD = 32;
|
|
63
|
+
// Z/H tag values are spec'd as printable ASCII, but a non-conforming writer
|
|
64
|
+
// would make the char-code path mis-decode UTF-8, so bail to TextDecoder on any
|
|
65
|
+
// high byte.
|
|
66
|
+
function decodeTagString(ba, start, end) {
|
|
67
|
+
const len = end - start;
|
|
68
|
+
if (len < SHORT_STRING_THRESHOLD) {
|
|
69
|
+
const codes = new Array(len);
|
|
70
|
+
for (let i = 0; i < len; i++) {
|
|
71
|
+
const byte = ba[start + i];
|
|
72
|
+
if (byte > 0x7f) {
|
|
73
|
+
return textDecoder.decode(ba.subarray(start, end));
|
|
74
|
+
}
|
|
75
|
+
codes[i] = byte;
|
|
76
|
+
}
|
|
77
|
+
return String.fromCharCode(...codes);
|
|
78
|
+
}
|
|
79
|
+
return textDecoder.decode(ba.subarray(start, end));
|
|
80
|
+
}
|
|
45
81
|
// Bitmask for ops that consume ref: M=0, D=2, N=3, P=6, ==7, X=8
|
|
46
82
|
// Binary: 0b111001101 = 0x1CD
|
|
47
83
|
const CIGAR_CONSUMES_REF_MASK = 0x1cd;
|
|
@@ -201,9 +237,7 @@ function decodeTagValue(ba, dataView, type, p, end, raw) {
|
|
|
201
237
|
return dataView.getFloat32(p, true);
|
|
202
238
|
case 0x5a: // 'Z'
|
|
203
239
|
case 0x48: // 'H'
|
|
204
|
-
return raw
|
|
205
|
-
? ba.subarray(p, end - 1)
|
|
206
|
-
: textDecoder.decode(ba.subarray(p, end - 1));
|
|
240
|
+
return raw ? ba.subarray(p, end - 1) : decodeTagString(ba, p, end - 1);
|
|
207
241
|
default: {
|
|
208
242
|
// 'B'
|
|
209
243
|
const Btype = ba[p];
|
|
@@ -224,12 +258,18 @@ export default class BamRecord {
|
|
|
224
258
|
_cachedNumericCigar;
|
|
225
259
|
_cachedNUMERIC_MD;
|
|
226
260
|
_cachedSeqStart;
|
|
227
|
-
|
|
228
|
-
|
|
229
|
-
|
|
230
|
-
|
|
231
|
-
|
|
232
|
-
|
|
261
|
+
// Positional rather than an options object, because every argument is
|
|
262
|
+
// unpacked into a field immediately and nothing keeps the wrapper. The
|
|
263
|
+
// options form allocated two throwaway objects for each of the ~200k records
|
|
264
|
+
// a deep pileup decodes — the `{byteArray, start, end}` literal and the
|
|
265
|
+
// `{bytes, fileOffset, dataView}` around it — purely to be taken apart again
|
|
266
|
+
// one line later.
|
|
267
|
+
constructor(byteArray, start, end, fileOffset, dataView) {
|
|
268
|
+
this._byteArray = byteArray;
|
|
269
|
+
this._start = start;
|
|
270
|
+
this._end = end;
|
|
271
|
+
this.fileOffset = fileOffset;
|
|
272
|
+
this._dataView = dataView;
|
|
233
273
|
}
|
|
234
274
|
get byteArray() {
|
|
235
275
|
return this._byteArray;
|
|
@@ -292,6 +332,13 @@ export default class BamRecord {
|
|
|
292
332
|
return this.seqStart + ((seqLen + 1) >> 1) + seqLen;
|
|
293
333
|
}
|
|
294
334
|
// batch fromCharCode: fastest for typical name lengths (see benchmarks/string-building.bench.ts)
|
|
335
|
+
//
|
|
336
|
+
// Deliberately NOT memoized, unlike end/tags/length_on_ref. Consumers read a
|
|
337
|
+
// read name about once — jbrowse-components' buildBaseFeatureData copies it
|
|
338
|
+
// straight into its own FeatureData — so a cache would pay a field slot on
|
|
339
|
+
// every record (+180KB per 22k-record chunk) to save zero decodes, and would
|
|
340
|
+
// pin every name string for as long as the chunk stays cached (+520KB) where
|
|
341
|
+
// today it dies with the consumer's copy.
|
|
295
342
|
get name() {
|
|
296
343
|
const len = this.read_name_length - 1;
|
|
297
344
|
const start = this.b0;
|
|
@@ -353,7 +400,7 @@ export default class BamRecord {
|
|
|
353
400
|
const tags = Object.create(null);
|
|
354
401
|
let p = this.tagsStart;
|
|
355
402
|
while (p < blockEnd) {
|
|
356
|
-
const tag =
|
|
403
|
+
const tag = tagName(ba[p], ba[p + 1]);
|
|
357
404
|
const type = ba[p + 2];
|
|
358
405
|
const valueStart = p + 3;
|
|
359
406
|
const end = tagValueEnd(ba, this._dataView, type, valueStart, blockEnd);
|