@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/esm/record.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
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1
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C,CAAC,CAAA;YAC1C,MAAM,KAAK,GAAG,IAAI,WAAW,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAChC,KAAK,CAAC,CAAC,CAAC,GAAG,iBAAiB,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAE,CAAE,CAAA;YAC3C,CAAC;YACD,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,GAAG,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,YAAY,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,MAAM,CAAE,GAAG,IAAI,CAAC,IAAI,CAAC,CAAE,CAAA;YAC7D,CAAC;YACD,GAAG,GAAG,WAAW,CAAC,MAAM,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAA;QAChD,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,4EAA4E;IAC5E,+EAA+E;IAC/E,+EAA+E;IAC/E,0CAA0C;IAC1C,EAAE;IACF,2EAA2E;IAC3E,8EAA8E;IAC9E,0EAA0E;IAC1E,8EAA8E;IAC9E,gCAAgC;IAChC,qEAAqE;IACrE,IAAI,gBAAgB;QAClB,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAA;QACpB,IAAI,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,WAAW,CAAC,EAAE,CAAC;YACjC,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,KAAK,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,MAAM,SAAS,GAAG,IAAI,CAAC,UAAU,CAAA;QACjC,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAA;QACtB,MAAM,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAA;QAC7B,MAAM,UAAU,GACd,KAAK,KAAK,SAAS;YACjB,CAAC,CAAC,KAAK,GAAG,SAAS;YACnB,CAAC,CAAC,GAAG,KAAK,OAAO;gBACf,CAAC,CAAC,GAAG,GAAG,OAAO;gBACf,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,UAAU,CAAC,CAAA;QACpC,OAAO,sBAAsB,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACxE,CAAC;IAED,IAAI,SAAS;QACX,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,IAAI,OAAO;QACT,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,IAAI,UAAU;QACZ,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,IAAI,UAAU;QACZ,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,IAAI,QAAQ;QACV,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,IAAI,eAAe;QACjB,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,GAAW;QACf,IAAI,GAAG,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC;YAC1B,MAAM,EAAE,GAAG,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,QAAQ,GAAG,CAAC,GAAG,IAAI,CAAC,CAAC,CAAE,CAAA;YAEvD,OAAO,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,CAAC;gBACpB,CAAC,CAAC,cAAc,CAAC,CAAC,EAAE,GAAG,IAAI,CAAC,IAAI,CAAC,CAAE;gBACnC,CAAC,CAAC,cAAc,CAAC,EAAE,GAAG,IAAI,CAAE,CAAA;QAChC,CAAC;aAAM,CAAC;YACN,OAAO,SAAS,CAAA;QAClB,CAAC;IACH,CAAC;IAED,gEAAgE;IAChE,6EAA6E;IAC7E,0EAA0E;IAC1E,2DAA2D;IAC3D,MAAM;QACJ,OAAO;YACL,UAAU,EAAE,IAAI,CAAC,UAAU;YAC3B,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,KAAK,EAAE,IAAI,CAAC,KAAK;YACjB,GAAG,EAAE,IAAI,CAAC,GAAG;YACb,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,KAAK,EAAE,IAAI,CAAC,KAAK;YACjB,EAAE,EAAE,IAAI,CAAC,EAAE;YACX,KAAK,EAAE,IAAI,CAAC,KAAK;YACjB,GAAG,EAAE,IAAI,CAAC,GAAG;YACb,UAAU,EAAE,IAAI,CAAC,UAAU;YAC3B,QAAQ,EAAE,IAAI,CAAC,QAAQ;YACvB,eAAe,EAAE,IAAI,CAAC,eAAe;YACrC,IAAI,EAAE,IAAI,CAAC,IAAI;SAChB,CAAA;IACH,CAAC;CACF"}
|
package/esm/util.d.ts
CHANGED
|
@@ -1,20 +1,10 @@
|
|
|
1
1
|
import Chunk from './chunk.ts';
|
|
2
2
|
import type { Offset, VirtualOffset } from './virtualOffset.ts';
|
|
3
|
-
export interface TagFilter {
|
|
4
|
-
tag: string;
|
|
5
|
-
value?: string;
|
|
6
|
-
}
|
|
7
|
-
export interface FilterBy {
|
|
8
|
-
flagInclude?: number;
|
|
9
|
-
flagExclude?: number;
|
|
10
|
-
tagFilter?: TagFilter;
|
|
11
|
-
}
|
|
12
3
|
export interface BamOpts {
|
|
13
4
|
viewAsPairs?: boolean;
|
|
14
5
|
pairAcrossChr?: boolean;
|
|
15
6
|
maxInsertSize?: number;
|
|
16
7
|
signal?: AbortSignal;
|
|
17
|
-
filterBy?: FilterBy;
|
|
18
8
|
/**
|
|
19
9
|
* Called as the BGZF blocks covering the query are fetched, with cumulative
|
|
20
10
|
* downloaded bytes and the total to fetch. Reported at block granularity (one
|
|
@@ -52,14 +42,6 @@ export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (a
|
|
|
52
42
|
refIdToName: string[];
|
|
53
43
|
};
|
|
54
44
|
export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;
|
|
55
|
-
export declare function filterReadFlag(flags: number, flagInclude: number, flagExclude: number): boolean;
|
|
56
|
-
export declare function filterTagValue(readVal: unknown, filterVal?: string): boolean;
|
|
57
|
-
interface Filterable {
|
|
58
|
-
flags: number;
|
|
59
|
-
tags: Record<string, unknown>;
|
|
60
|
-
getTag?(tag: string): unknown;
|
|
61
|
-
}
|
|
62
|
-
export declare function applyFilters<T extends Filterable>(records: T[], filterBy: FilterBy): T[];
|
|
63
45
|
interface Positioned {
|
|
64
46
|
ref_id: number;
|
|
65
47
|
start: number;
|
package/esm/util.js
CHANGED
|
@@ -167,33 +167,6 @@ export function concatUint8Array(args) {
|
|
|
167
167
|
}
|
|
168
168
|
return mergedArray;
|
|
169
169
|
}
|
|
170
|
-
export function filterReadFlag(flags, flagInclude, flagExclude) {
|
|
171
|
-
return (flags & flagInclude) !== flagInclude || (flags & flagExclude) !== 0;
|
|
172
|
-
}
|
|
173
|
-
export function filterTagValue(readVal, filterVal) {
|
|
174
|
-
return filterVal === '*'
|
|
175
|
-
? readVal === undefined
|
|
176
|
-
: `${readVal}` !== `${filterVal}`;
|
|
177
|
-
}
|
|
178
|
-
// Read a single tag, preferring the targeted accessor. Reaching for `tags`
|
|
179
|
-
// instead would decode every unrelated tag on the record (NM/AS/ms/de/… — often
|
|
180
|
-
// ~10 per read) just to test one, which measured 2.6x the cost of getTag.
|
|
181
|
-
function readTag(record, tag) {
|
|
182
|
-
return record.getTag ? record.getTag(tag) : record.tags[tag];
|
|
183
|
-
}
|
|
184
|
-
// Apply flagInclude/flagExclude/tagFilter to a list of records.
|
|
185
|
-
export function applyFilters(records, filterBy) {
|
|
186
|
-
const { flagInclude = 0, flagExclude = 0, tagFilter } = filterBy;
|
|
187
|
-
const out = [];
|
|
188
|
-
for (let i = 0, l = records.length; i < l; i++) {
|
|
189
|
-
const r = records[i];
|
|
190
|
-
if (!filterReadFlag(r.flags, flagInclude, flagExclude) &&
|
|
191
|
-
!(tagFilter && filterTagValue(readTag(r, tagFilter.tag), tagFilter.value))) {
|
|
192
|
-
out.push(r);
|
|
193
|
-
}
|
|
194
|
-
}
|
|
195
|
-
return out;
|
|
196
|
-
}
|
|
197
170
|
// Append records overlapping [min, max) on `chrId` into `out` (or a fresh
|
|
198
171
|
// array if omitted). Records are assumed coordinate-sorted (by ref_id, then
|
|
199
172
|
// start), so we stop scanning once we pass `max` within `chrId` or move past
|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AA8BnD,MAAM,UAAU,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,KAAK,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,MAAM,UAAU,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO;QACL,SAAS,EAAE,uBAAuB,CAAC,KAAK,EAAE,MAAM,CAAC;KAClD,CAAA;AACH,CAAC;AAED,6EAA6E;AAC7E,kFAAkF;AAClF,kFAAkF;AAClF,iFAAiF;AACjF,kFAAkF;AAClF,iFAAiF;AACjF,yEAAyE;AACzE,MAAM,UAAU,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,MAAM,UAAU,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,MAAM,UAAU,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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|
package/package.json
CHANGED
package/src/bamFile.ts
CHANGED
|
@@ -7,10 +7,9 @@ import CSI from './csi.ts'
|
|
|
7
7
|
import NullFilehandle from './nullFilehandle.ts'
|
|
8
8
|
import BAMFeature from './record.ts'
|
|
9
9
|
import { parseHeaderText } from './sam.ts'
|
|
10
|
-
import { appendInRange,
|
|
10
|
+
import { appendInRange, parseRefSeqs } from './util.ts'
|
|
11
11
|
|
|
12
12
|
import type Chunk from './chunk.ts'
|
|
13
|
-
import type { Bytes } from './record.ts'
|
|
14
13
|
import type { BamOpts, BaseOpts } from './util.ts'
|
|
15
14
|
import type { GenericFilehandle } from 'generic-filehandle2'
|
|
16
15
|
|
|
@@ -26,11 +25,13 @@ export interface BamRecordLike {
|
|
|
26
25
|
tags: Record<string, unknown>
|
|
27
26
|
}
|
|
28
27
|
|
|
29
|
-
export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
|
|
33
|
-
|
|
28
|
+
export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (
|
|
29
|
+
byteArray: Uint8Array,
|
|
30
|
+
start: number,
|
|
31
|
+
end: number,
|
|
32
|
+
fileOffset: number,
|
|
33
|
+
dataView: DataView,
|
|
34
|
+
) => T
|
|
34
35
|
|
|
35
36
|
export const BAM_MAGIC = 21840194
|
|
36
37
|
|
|
@@ -48,17 +49,18 @@ function resolveFilehandle(
|
|
|
48
49
|
}
|
|
49
50
|
|
|
50
51
|
interface ChunkEntry<T> {
|
|
51
|
-
minBlock: number
|
|
52
|
-
maxBlock: number
|
|
53
52
|
// decompressed size of the chunk these features are views into
|
|
54
53
|
bytes: number
|
|
55
54
|
features: T[]
|
|
56
55
|
}
|
|
57
56
|
|
|
58
|
-
|
|
59
|
-
|
|
60
|
-
//
|
|
61
|
-
//
|
|
57
|
+
interface InFlightChunk<T> {
|
|
58
|
+
promise: Promise<ChunkEntry<T>>
|
|
59
|
+
// the signal the read was started with, so a waiter can tell "the owner
|
|
60
|
+
// aborted" apart from "the read genuinely failed"
|
|
61
|
+
signal?: AbortSignal
|
|
62
|
+
}
|
|
63
|
+
|
|
62
64
|
function chunkCacheKey(chunk: Chunk) {
|
|
63
65
|
const { minv, maxv } = chunk
|
|
64
66
|
return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`
|
|
@@ -68,9 +70,16 @@ function chunkCacheKey(chunk: Chunk) {
|
|
|
68
70
|
// caching one entry pins that whole buffer — 8MB apiece on the nanopore and
|
|
69
71
|
// 2kb-read test files, and optimizeChunks merges spans up to 5MB *compressed*,
|
|
70
72
|
// so tens of MB is possible. A count-based LRU therefore gives no bound on
|
|
71
|
-
// memory at all, which is why this budgets by decompressed bytes instead.
|
|
73
|
+
// memory at all, which is why this budgets by decompressed bytes instead. It is
|
|
74
|
+
// the *only* bound: a query keeps every chunk it parsed, since a chunk dropped
|
|
75
|
+
// here costs a re-download and re-decompress the next time the view moves.
|
|
72
76
|
export const DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024
|
|
73
77
|
|
|
78
|
+
// How many of a query's chunks to read at once. Six is the HTTP/1.1
|
|
79
|
+
// per-host connection cap browsers enforce, so going much above it buys
|
|
80
|
+
// nothing on the transport that matters and only widens peak memory.
|
|
81
|
+
const MAX_CONCURRENT_CHUNK_READS = 6
|
|
82
|
+
|
|
74
83
|
class ChunkFeatureCache<T> {
|
|
75
84
|
public maxBytes: number
|
|
76
85
|
private entries = new Map<string, ChunkEntry<T>>()
|
|
@@ -139,10 +148,14 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
139
148
|
public htsget = false
|
|
140
149
|
public headerP?: ReturnType<BamFile<T>['getHeaderPre']>
|
|
141
150
|
|
|
142
|
-
// Cache for parsed features by chunk
|
|
143
|
-
// When a new chunk overlaps a cached chunk, we evict the cached one
|
|
151
|
+
// Cache for parsed features by chunk, bounded by decompressed bytes
|
|
144
152
|
public chunkFeatureCache: ChunkFeatureCache<T>
|
|
145
153
|
|
|
154
|
+
// Chunks currently being read, so concurrent queries share one decompress
|
|
155
|
+
// instead of racing. Entries live only until the read settles; the resolved
|
|
156
|
+
// features land in chunkFeatureCache.
|
|
157
|
+
private inFlightChunks = new Map<string, InFlightChunk<T>>()
|
|
158
|
+
|
|
146
159
|
private RecordClass: BamRecordClass<T>
|
|
147
160
|
|
|
148
161
|
constructor({
|
|
@@ -281,6 +294,15 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
281
294
|
return this.chrToIndex?.[seqName]
|
|
282
295
|
}
|
|
283
296
|
|
|
297
|
+
/**
|
|
298
|
+
* Records overlapping `chr:min-max`.
|
|
299
|
+
*
|
|
300
|
+
* The returned records are CACHED AND SHARED — two queries resolving to the
|
|
301
|
+
* same chunk span get the same objects back, so treat them as read-only.
|
|
302
|
+
* Anything you want to attach for the duration of one query belongs on a
|
|
303
|
+
* wrapper you own, never on the record; writing a field here silently rebinds
|
|
304
|
+
* it for every other query still holding that read. See ADR 0006.
|
|
305
|
+
*/
|
|
284
306
|
async getRecordsForRange(
|
|
285
307
|
chr: string,
|
|
286
308
|
min: number,
|
|
@@ -295,12 +317,69 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
295
317
|
return this._fetchChunkFeatures(chunks, chrId, min, max, opts)
|
|
296
318
|
}
|
|
297
319
|
|
|
298
|
-
//
|
|
299
|
-
|
|
300
|
-
|
|
301
|
-
|
|
302
|
-
|
|
320
|
+
// Read a chunk, publish it to the cache, and keep the in-flight promise
|
|
321
|
+
// discoverable while it runs.
|
|
322
|
+
private _startChunkRead(cacheKey: string, chunk: Chunk, opts: BaseOpts) {
|
|
323
|
+
const promise = this._readChunkFeatures(chunk, opts).then(entry => {
|
|
324
|
+
this.chunkFeatureCache.set(cacheKey, entry)
|
|
325
|
+
return entry
|
|
326
|
+
})
|
|
327
|
+
const inFlight: InFlightChunk<T> = { promise, signal: opts.signal }
|
|
328
|
+
this.inFlightChunks.set(cacheKey, inFlight)
|
|
329
|
+
// Only clear our own entry: a retry may already have replaced it. `.then(f,
|
|
330
|
+
// f)` rather than `.finally(f)` so the handler's own promise never carries
|
|
331
|
+
// an unhandled rejection.
|
|
332
|
+
const clear = () => {
|
|
333
|
+
if (this.inFlightChunks.get(cacheKey) === inFlight) {
|
|
334
|
+
this.inFlightChunks.delete(cacheKey)
|
|
335
|
+
}
|
|
336
|
+
}
|
|
337
|
+
promise.then(clear, clear)
|
|
338
|
+
return promise
|
|
339
|
+
}
|
|
340
|
+
|
|
341
|
+
// Parsed records for a chunk, reading and decompressing it only on a miss.
|
|
342
|
+
// Every path that wants a chunk's features goes through here — mate lookups
|
|
343
|
+
// included, since a viewAsPairs query revisits the same mate chunks each time
|
|
344
|
+
// the view moves.
|
|
345
|
+
//
|
|
346
|
+
// This hands the SAME record objects to every query that hits the key, which
|
|
347
|
+
// is what makes callers' per-query writes onto a record leak across queries
|
|
348
|
+
// (ADR 0006). Caching the inflated buffer and re-scanning per query would give
|
|
349
|
+
// each caller its own objects, but roughly doubles a warm query on dense data
|
|
350
|
+
// — measured, and rejected, in that ADR.
|
|
351
|
+
private async _cachedChunkFeatures(
|
|
352
|
+
chunk: Chunk,
|
|
353
|
+
opts: BaseOpts,
|
|
354
|
+
): Promise<T[]> {
|
|
355
|
+
const cacheKey = chunkCacheKey(chunk)
|
|
356
|
+
const cached = this.chunkFeatureCache.get(cacheKey)
|
|
357
|
+
if (cached) {
|
|
358
|
+
return cached.features
|
|
359
|
+
}
|
|
360
|
+
|
|
361
|
+
// Join a read already running for this chunk rather than decompressing it a
|
|
362
|
+
// second time. jbrowse fetches a row of adjacent blocks concurrently and
|
|
363
|
+
// they collapse onto very few chunk keys, so without this a query pays for
|
|
364
|
+
// the same inflate several times over — the dominant cost of a cold query
|
|
365
|
+
// (ADR 0003).
|
|
366
|
+
const pending = this.inFlightChunks.get(cacheKey)
|
|
367
|
+
if (!pending) {
|
|
368
|
+
return (await this._startChunkRead(cacheKey, chunk, opts)).features
|
|
369
|
+
}
|
|
370
|
+
|
|
371
|
+
try {
|
|
372
|
+
return (await pending.promise).features
|
|
373
|
+
} catch (e) {
|
|
374
|
+
// The read we joined was started by another caller. If that caller
|
|
375
|
+
// aborted and we did not, the failure is theirs and says nothing about
|
|
376
|
+
// our query, so start over — which picks up the cache, joins a sibling's
|
|
377
|
+
// retry, or reads under our own signal. Any other failure (and our own
|
|
378
|
+
// abort) propagates as it would have without sharing.
|
|
379
|
+
if (!pending.signal?.aborted || opts.signal?.aborted) {
|
|
380
|
+
throw e
|
|
303
381
|
}
|
|
382
|
+
return this._cachedChunkFeatures(chunk, opts)
|
|
304
383
|
}
|
|
305
384
|
}
|
|
306
385
|
|
|
@@ -311,7 +390,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
311
390
|
max: number,
|
|
312
391
|
opts: BamOpts = {},
|
|
313
392
|
) {
|
|
314
|
-
const { viewAsPairs,
|
|
393
|
+
const { viewAsPairs, onProgress } = opts
|
|
315
394
|
const result: T[] = []
|
|
316
395
|
|
|
317
396
|
let totalBytes = 0
|
|
@@ -321,26 +400,42 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
321
400
|
let downloadedBytes = 0
|
|
322
401
|
onProgress?.(0, totalBytes)
|
|
323
402
|
|
|
324
|
-
|
|
325
|
-
|
|
326
|
-
|
|
327
|
-
|
|
328
|
-
|
|
329
|
-
|
|
330
|
-
|
|
331
|
-
|
|
332
|
-
|
|
333
|
-
|
|
334
|
-
|
|
335
|
-
|
|
403
|
+
const featureLists = new Array<T[]>(chunks.length)
|
|
404
|
+
if (chunks.length === 1) {
|
|
405
|
+
// Very common — most small files, and any query landing inside one bin.
|
|
406
|
+
// Worth its own path: the pool below allocates a closure, a worker array
|
|
407
|
+
// and a Promise.all, all of which is pure overhead for one chunk and
|
|
408
|
+
// measurable on queries that take ~0.2ms.
|
|
409
|
+
featureLists[0] = await this._cachedChunkFeatures(chunks[0]!, opts)
|
|
410
|
+
onProgress?.(totalBytes, totalBytes)
|
|
411
|
+
} else {
|
|
412
|
+
// Fetch the chunks concurrently. A query routinely spans a dozen or more
|
|
413
|
+
// chunks (14.8 on average for a 20kb window on the test 18MB file) and
|
|
414
|
+
// each is its own range request, so reading them one after another costs
|
|
415
|
+
// a network round trip apiece — the dominant cost of a remote query, well
|
|
416
|
+
// ahead of decompression. Bounded because browsers cap concurrent
|
|
417
|
+
// connections per host anyway, and an unbounded fan-out would inflate
|
|
418
|
+
// every chunk of a whole-chromosome query at once.
|
|
419
|
+
let next = 0
|
|
420
|
+
const readNext = async () => {
|
|
421
|
+
while (next < chunks.length) {
|
|
422
|
+
const ci = next++
|
|
423
|
+
const chunk = chunks[ci]!
|
|
424
|
+
featureLists[ci] = await this._cachedChunkFeatures(chunk, opts)
|
|
425
|
+
downloadedBytes += chunk.fetchedSize()
|
|
426
|
+
onProgress?.(downloadedBytes, totalBytes)
|
|
427
|
+
}
|
|
336
428
|
}
|
|
337
|
-
const
|
|
338
|
-
|
|
339
|
-
|
|
429
|
+
const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length)
|
|
430
|
+
await Promise.all(Array.from({ length: workers }, () => readNext()))
|
|
431
|
+
}
|
|
340
432
|
|
|
341
|
-
|
|
342
|
-
|
|
343
|
-
|
|
433
|
+
// Append in chunk order, not completion order, so the result is the same
|
|
434
|
+
// sequence a sequential walk produced. (That is not coordinate order — bins
|
|
435
|
+
// at different levels cover overlapping spans — but it is what every caller
|
|
436
|
+
// has always been handed.)
|
|
437
|
+
for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
|
|
438
|
+
appendInRange(featureLists[ci]!, chrId, min, max, result)
|
|
344
439
|
}
|
|
345
440
|
|
|
346
441
|
if (viewAsPairs) {
|
|
@@ -402,7 +497,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
402
497
|
|
|
403
498
|
const mateFeatLists = await Promise.all(
|
|
404
499
|
[...map.values()].map(async c => {
|
|
405
|
-
const
|
|
500
|
+
const features = await this._cachedChunkFeatures(c, opts)
|
|
406
501
|
const mateRecs = [] as T[]
|
|
407
502
|
for (let i = 0, l = features.length; i < l; i++) {
|
|
408
503
|
const feature = features[i]!
|
|
@@ -469,20 +564,18 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
469
564
|
}
|
|
470
565
|
|
|
471
566
|
if (blockEnd < ba.length) {
|
|
472
|
-
const feature = new this.RecordClass(
|
|
473
|
-
|
|
474
|
-
|
|
475
|
-
|
|
476
|
-
|
|
477
|
-
},
|
|
478
|
-
fileOffset: hasCpositions
|
|
567
|
+
const feature = new this.RecordClass(
|
|
568
|
+
ba,
|
|
569
|
+
blockStart,
|
|
570
|
+
blockEnd,
|
|
571
|
+
hasCpositions
|
|
479
572
|
? cpositions[pos]! * (1 << 8) +
|
|
480
573
|
(blockStart - dpositions[pos]!) +
|
|
481
574
|
chunk.minv.dataPosition +
|
|
482
575
|
1
|
|
483
576
|
: crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
|
|
484
577
|
dataView,
|
|
485
|
-
|
|
578
|
+
)
|
|
486
579
|
|
|
487
580
|
sink.push(feature)
|
|
488
581
|
}
|
package/src/index.ts
CHANGED
package/src/record.ts
CHANGED
|
@@ -48,6 +48,45 @@ const ASCII_CIGAR_CODES = [
|
|
|
48
48
|
|
|
49
49
|
const textDecoder = new TextDecoder()
|
|
50
50
|
|
|
51
|
+
// Interned two-char tag names keyed on the packed byte pair. Worth more than
|
|
52
|
+
// the saved String.fromCharCode: the tags object is null-prototype and so in
|
|
53
|
+
// dictionary mode, and handing it a string V8 has already hashed halves the
|
|
54
|
+
// per-tag insert cost.
|
|
55
|
+
const TAG_NAMES = new Map<number, string>()
|
|
56
|
+
function tagName(b0: number, b1: number) {
|
|
57
|
+
const key = (b0 << 8) | b1
|
|
58
|
+
let name = TAG_NAMES.get(key)
|
|
59
|
+
if (name === undefined) {
|
|
60
|
+
name = String.fromCharCode(b0, b1)
|
|
61
|
+
TAG_NAMES.set(key, name)
|
|
62
|
+
}
|
|
63
|
+
return name
|
|
64
|
+
}
|
|
65
|
+
|
|
66
|
+
// TextDecoder carries ~0.35us of fixed setup per call, which dominates for the
|
|
67
|
+
// short values Z/H tags usually hold (MD, RG, PG, ...): char codes are 4x
|
|
68
|
+
// faster at 8 bytes, 2x at 16, and the two cross over at 32.
|
|
69
|
+
const SHORT_STRING_THRESHOLD = 32
|
|
70
|
+
|
|
71
|
+
// Z/H tag values are spec'd as printable ASCII, but a non-conforming writer
|
|
72
|
+
// would make the char-code path mis-decode UTF-8, so bail to TextDecoder on any
|
|
73
|
+
// high byte.
|
|
74
|
+
function decodeTagString(ba: Uint8Array, start: number, end: number) {
|
|
75
|
+
const len = end - start
|
|
76
|
+
if (len < SHORT_STRING_THRESHOLD) {
|
|
77
|
+
const codes = new Array<number>(len)
|
|
78
|
+
for (let i = 0; i < len; i++) {
|
|
79
|
+
const byte = ba[start + i]!
|
|
80
|
+
if (byte > 0x7f) {
|
|
81
|
+
return textDecoder.decode(ba.subarray(start, end))
|
|
82
|
+
}
|
|
83
|
+
codes[i] = byte
|
|
84
|
+
}
|
|
85
|
+
return String.fromCharCode(...codes)
|
|
86
|
+
}
|
|
87
|
+
return textDecoder.decode(ba.subarray(start, end))
|
|
88
|
+
}
|
|
89
|
+
|
|
51
90
|
// Bitmask for ops that consume ref: M=0, D=2, N=3, P=6, ==7, X=8
|
|
52
91
|
// Binary: 0b111001101 = 0x1CD
|
|
53
92
|
const CIGAR_CONSUMES_REF_MASK = 0x1cd
|
|
@@ -252,9 +291,7 @@ function decodeTagValue(
|
|
|
252
291
|
return dataView.getFloat32(p, true)
|
|
253
292
|
case 0x5a: // 'Z'
|
|
254
293
|
case 0x48: // 'H'
|
|
255
|
-
return raw
|
|
256
|
-
? ba.subarray(p, end - 1)
|
|
257
|
-
: textDecoder.decode(ba.subarray(p, end - 1))
|
|
294
|
+
return raw ? ba.subarray(p, end - 1) : decodeTagString(ba, p, end - 1)
|
|
258
295
|
default: {
|
|
259
296
|
// 'B'
|
|
260
297
|
const Btype = ba[p]!
|
|
@@ -278,12 +315,24 @@ export default class BamRecord {
|
|
|
278
315
|
private _cachedNUMERIC_MD?: Uint8Array | null
|
|
279
316
|
private _cachedSeqStart?: number
|
|
280
317
|
|
|
281
|
-
|
|
282
|
-
|
|
283
|
-
|
|
284
|
-
|
|
285
|
-
|
|
286
|
-
|
|
318
|
+
// Positional rather than an options object, because every argument is
|
|
319
|
+
// unpacked into a field immediately and nothing keeps the wrapper. The
|
|
320
|
+
// options form allocated two throwaway objects for each of the ~200k records
|
|
321
|
+
// a deep pileup decodes — the `{byteArray, start, end}` literal and the
|
|
322
|
+
// `{bytes, fileOffset, dataView}` around it — purely to be taken apart again
|
|
323
|
+
// one line later.
|
|
324
|
+
constructor(
|
|
325
|
+
byteArray: Uint8Array,
|
|
326
|
+
start: number,
|
|
327
|
+
end: number,
|
|
328
|
+
fileOffset: number,
|
|
329
|
+
dataView: DataView,
|
|
330
|
+
) {
|
|
331
|
+
this._byteArray = byteArray
|
|
332
|
+
this._start = start
|
|
333
|
+
this._end = end
|
|
334
|
+
this.fileOffset = fileOffset
|
|
335
|
+
this._dataView = dataView
|
|
287
336
|
}
|
|
288
337
|
|
|
289
338
|
get byteArray() {
|
|
@@ -358,6 +407,13 @@ export default class BamRecord {
|
|
|
358
407
|
}
|
|
359
408
|
|
|
360
409
|
// batch fromCharCode: fastest for typical name lengths (see benchmarks/string-building.bench.ts)
|
|
410
|
+
//
|
|
411
|
+
// Deliberately NOT memoized, unlike end/tags/length_on_ref. Consumers read a
|
|
412
|
+
// read name about once — jbrowse-components' buildBaseFeatureData copies it
|
|
413
|
+
// straight into its own FeatureData — so a cache would pay a field slot on
|
|
414
|
+
// every record (+180KB per 22k-record chunk) to save zero decodes, and would
|
|
415
|
+
// pin every name string for as long as the chunk stays cached (+520KB) where
|
|
416
|
+
// today it dies with the consumer's copy.
|
|
361
417
|
get name() {
|
|
362
418
|
const len = this.read_name_length - 1
|
|
363
419
|
const start = this.b0
|
|
@@ -425,7 +481,7 @@ export default class BamRecord {
|
|
|
425
481
|
const tags: Record<string, unknown> = Object.create(null)
|
|
426
482
|
let p = this.tagsStart
|
|
427
483
|
while (p < blockEnd) {
|
|
428
|
-
const tag =
|
|
484
|
+
const tag = tagName(ba[p]!, ba[p + 1]!)
|
|
429
485
|
const type = ba[p + 2]!
|
|
430
486
|
const valueStart = p + 3
|
|
431
487
|
const end = tagValueEnd(ba, this._dataView, type, valueStart, blockEnd)
|