@gmod/bam 8.7.0 → 8.8.1
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/dist/bamFile.d.ts +14 -0
- package/dist/bamFile.js.map +1 -1
- package/dist/index.d.ts +1 -1
- package/dist/index.js +6 -1
- package/dist/index.js.map +1 -1
- package/esm/bamFile.d.ts +14 -0
- package/esm/bamFile.js.map +1 -1
- package/esm/index.d.ts +1 -1
- package/esm/index.js +4 -1
- package/esm/index.js.map +1 -1
- package/package.json +2 -2
- package/src/bamFile.ts +14 -0
- package/src/index.ts +8 -1
package/dist/bamFile.d.ts
CHANGED
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@@ -164,6 +164,20 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
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164
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* has long since resolved. `undefined` (which is what that helper gives
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165
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* back under node, or anywhere Workers cannot be created) keeps the
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* in-process path, so this is safe to pass unconditionally.
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167
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+
*
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168
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+
* **Holding a pool for the life of this object is fine, and deliberately
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169
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* so.** It is stored here and awaited once per chunk read, which used to
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170
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* mean four workers and their grow-only wasm heaps stayed up from the first
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171
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* query until the page went away. As of `@gmod/bgzf-filehandle` 6.6.0 a
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172
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* pool reaps its own workers after 3 minutes idle and spawns a fresh set on
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173
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* the next call, and that is invisible from here — the pool object stays
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174
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* valid throughout.
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175
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+
*
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* Which is also why a caller must NOT try to reclaim it by calling
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177
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* `destroySharedWorkerPool()` on an idle timer of its own: a destroyed pool
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* throws out of `decompressBlocks`, so every open `BamFile` still holding
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179
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* one would fail its next read rather than fall back to inflating in
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180
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* process. Reclaiming is the pool's job, not the consumer's.
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167
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*/
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bgzfWorkerPool?: BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined;
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169
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/**
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package/dist/bamFile.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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+
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M;SACpB,CACF,CAAA;QACD,0EAA0E;QAC1E,oEAAoE;QACpE,2EAA2E;QAC3E,yEAAyE;QACzE,4EAA4E;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,oEAAoE;QACpE,EAAE;QACF,uEAAuE;QACvE,sEAAsE;QACtE,2EAA2E;QAC3E,sEAAsE;QACtE,IAAA,wBAAc,EAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAE3B,wEAAwE;QACxE,qEAAqE;QACrE,6CAA6C;QAC7C,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QACtC,MAAM,EACJ,MAAM,EAAE,IAAI,EACZ,UAAU,EACV,UAAU,GACX,GAAG,MAAM,IAAA,iCAAe,EAAC,GAAG,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;QAC3C,OAAO;YACL,QAAQ,EAAE,IAAI,CAAC,eAAe,CAAC,IAAI,EAAE,UAAU,EAAE,UAAU,EAAE,KAAK,CAAC;YACnE,KAAK,EAAE,IAAI,CAAC,UAAU;SACvB,CAAA;IACH,CAAC;IAED,0EAA0E;IAC1E,8EAA8E;IAC9E,8EAA8E;IAC9E,sEAAsE;IACtE,uCAAuC;IACvC,eAAe,CACb,EAAc,EACd,UAA6B,EAC7B,UAA6B,EAC7B,KAAY;QAEZ,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,MAAM,IAAI,GAAG,EAAS,CAAA;QACtB,IAAI,GAAG,GAAG,CAAC,CAAA;QAEX,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,CAAC,MAAM,EAAE,EAAE,CAAC,UAAU,EAAE,EAAE,CAAC,UAAU,CAAC,CAAA;QACtE,MAAM,aAAa,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAC3C,MAAM,aAAa,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAE3C,OAAO,UAAU,GAAG,CAAC,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC;YAClC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;YACrD,MAAM,QAAQ,GAAG,UAAU,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,CAAA;YAE/C,IAAI,aAAa,EAAE,CAAC;gBAClB,MAAM,MAAM,GAAG,UAAU,GAAG,KAAK,CAAC,IAAI,CAAC,YAAY,CAAA;gBACnD,OAAO,GAAG,GAAG,UAAU,CAAC,MAAM,IAAI,MAAM,IAAI,UAAU,CAAC,GAAG,CAAE,EAAE,CAAC;oBAC7D,GAAG,EAAE,CAAA;gBACP,CAAC;YACH,CAAC;YAED,IAAI,QAAQ,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC;gBACzB,MAAM,OAAO,GAAG,IAAI,IAAI,CAAC,WAAW,CAClC,EAAE,EACF,UAAU,EACV,QAAQ,EACR,aAAa;oBACX,CAAC,CAAC,UAAU,CAAC,GAAG,CAAE,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;wBACzB,CAAC,UAAU,GAAG,UAAU,CAAC,GAAG,CAAE,CAAC;wBAC/B,KAAK,CAAC,IAAI,CAAC,YAAY;wBACvB,CAAC;oBACL,CAAC,CAAC,IAAA,eAAK,EAAC,EAAE,CAAC,QAAQ,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC,KAAK,CAAC,EAClD,QAAQ,CACT,CAAA;gBAED,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACpB,CAAC;YAED,UAAU,GAAG,QAAQ,GAAG,CAAC,CAAA;QAC3B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,IAAe;QAC9C,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QAChD,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS;YACvC,CAAC,CAAC,KAAK;YACP,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;IACjC,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,IAAe;QAC9C,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QAChD,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;IAC7E,CAAC;IAED,KAAK,CAAC,QAAQ,CAAC,OAAe,EAAE,KAAc,EAAE,GAAY;QAC1D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAA;QAC1C,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS;YACvC,CAAC,CAAC,EAAE;YACJ,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,OAAe,EACf,KAAa,EACb,GAAW,EACX,IAAe;QAEf,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QAChD,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS;YACvC,CAAC,CAAC,EAAE;YACJ,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,iBAAiB;QACf,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,CAAA;IAChC,CAAC;IAED,KAAK,CAAC,wBAAwB,CAC5B,OAA0D,EAC1D,IAAe;QAEf,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YAChB,OAAO,CAAC,CAAA;QACV,CAAC;QACD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACjC,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;YAC1C,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,GAAG,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QAC3E,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,KAAK,CAAC,wBAAwB,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAC1D,CAAC;CACF;AAr0BD,0BAq0BC"}
|
package/dist/index.d.ts
CHANGED
|
@@ -4,7 +4,7 @@ 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 { MISMATCH_DELETION, MISMATCH_HARD_CLIP, MISMATCH_INSERTION, MISMATCH_REF_SKIP, MISMATCH_SOFT_CLIP, MISMATCH_SUBST, forEachMismatchNumeric, } from './mismatches.ts';
|
|
7
|
-
export { packReference } from './reference.ts';
|
|
7
|
+
export { CHAR_CODE_FROM_NIBBLE, packReference, referenceNibble, } from './reference.ts';
|
|
8
8
|
export type { NumericCigar } from './record.ts';
|
|
9
9
|
export type { BamRecordClass, BamRecordLike, ReferenceSequenceFetcher, } from './bamFile.ts';
|
|
10
10
|
export type { Mismatch, MismatchCallback, MismatchOptions, } from './mismatches.ts';
|
package/dist/index.js
CHANGED
|
@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
-
exports.packReference = exports.forEachMismatchNumeric = exports.MISMATCH_SUBST = exports.MISMATCH_SOFT_CLIP = exports.MISMATCH_REF_SKIP = exports.MISMATCH_INSERTION = exports.MISMATCH_HARD_CLIP = exports.MISMATCH_DELETION = exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.DEFAULT_MAX_CACHE_BYTES = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.BAI = void 0;
|
|
6
|
+
exports.referenceNibble = exports.packReference = exports.CHAR_CODE_FROM_NIBBLE = exports.forEachMismatchNumeric = exports.MISMATCH_SUBST = exports.MISMATCH_SOFT_CLIP = exports.MISMATCH_REF_SKIP = exports.MISMATCH_INSERTION = exports.MISMATCH_HARD_CLIP = exports.MISMATCH_DELETION = exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.DEFAULT_MAX_CACHE_BYTES = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.BAI = void 0;
|
|
7
7
|
var bai_ts_1 = require("./bai.js");
|
|
8
8
|
Object.defineProperty(exports, "BAI", { enumerable: true, get: function () { return __importDefault(bai_ts_1).default; } });
|
|
9
9
|
var bamFile_ts_1 = require("./bamFile.js");
|
|
@@ -28,6 +28,11 @@ Object.defineProperty(exports, "MISMATCH_REF_SKIP", { enumerable: true, get: fun
|
|
|
28
28
|
Object.defineProperty(exports, "MISMATCH_SOFT_CLIP", { enumerable: true, get: function () { return mismatches_ts_1.MISMATCH_SOFT_CLIP; } });
|
|
29
29
|
Object.defineProperty(exports, "MISMATCH_SUBST", { enumerable: true, get: function () { return mismatches_ts_1.MISMATCH_SUBST; } });
|
|
30
30
|
Object.defineProperty(exports, "forEachMismatchNumeric", { enumerable: true, get: function () { return mismatches_ts_1.forEachMismatchNumeric; } });
|
|
31
|
+
// `referenceNibble` and `CHAR_CODE_FROM_NIBBLE` are what read a base back out
|
|
32
|
+
// of a packed region — a consumer that holds one otherwise has no way to see
|
|
33
|
+
// what is in it, which makes a binding untestable from the outside.
|
|
31
34
|
var reference_ts_1 = require("./reference.js");
|
|
35
|
+
Object.defineProperty(exports, "CHAR_CODE_FROM_NIBBLE", { enumerable: true, get: function () { return reference_ts_1.CHAR_CODE_FROM_NIBBLE; } });
|
|
32
36
|
Object.defineProperty(exports, "packReference", { enumerable: true, get: function () { return reference_ts_1.packReference; } });
|
|
37
|
+
Object.defineProperty(exports, "referenceNibble", { enumerable: true, get: function () { return reference_ts_1.referenceNibble; } });
|
|
33
38
|
//# sourceMappingURL=index.js.map
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAIqB;AAHnB,2HAAA,6BAA6B,OAAA;AAC7B,qHAAA,uBAAuB,OAAA;AACvB,sHAAA,OAAO,OAAW;AAEpB,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc;AAE9B,0EAA0E;AAC1E,+EAA+E;AAC/E,2EAA2E;AAC3E,2BAA2B;AAC3B,iDAQwB;AAPtB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,mHAAA,kBAAkB,OAAA;AAClB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,+GAAA,cAAc,OAAA;AACd,uHAAA,sBAAsB,OAAA;AAExB,+
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAIqB;AAHnB,2HAAA,6BAA6B,OAAA;AAC7B,qHAAA,uBAAuB,OAAA;AACvB,sHAAA,OAAO,OAAW;AAEpB,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc;AAE9B,0EAA0E;AAC1E,+EAA+E;AAC/E,2EAA2E;AAC3E,2BAA2B;AAC3B,iDAQwB;AAPtB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,mHAAA,kBAAkB,OAAA;AAClB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,+GAAA,cAAc,OAAA;AACd,uHAAA,sBAAsB,OAAA;AAExB,8EAA8E;AAC9E,6EAA6E;AAC7E,oEAAoE;AACpE,+CAIuB;AAHrB,qHAAA,qBAAqB,OAAA;AACrB,6GAAA,aAAa,OAAA;AACb,+GAAA,eAAe,OAAA"}
|
package/esm/bamFile.d.ts
CHANGED
|
@@ -164,6 +164,20 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
164
164
|
* has long since resolved. `undefined` (which is what that helper gives
|
|
165
165
|
* back under node, or anywhere Workers cannot be created) keeps the
|
|
166
166
|
* in-process path, so this is safe to pass unconditionally.
|
|
167
|
+
*
|
|
168
|
+
* **Holding a pool for the life of this object is fine, and deliberately
|
|
169
|
+
* so.** It is stored here and awaited once per chunk read, which used to
|
|
170
|
+
* mean four workers and their grow-only wasm heaps stayed up from the first
|
|
171
|
+
* query until the page went away. As of `@gmod/bgzf-filehandle` 6.6.0 a
|
|
172
|
+
* pool reaps its own workers after 3 minutes idle and spawns a fresh set on
|
|
173
|
+
* the next call, and that is invisible from here — the pool object stays
|
|
174
|
+
* valid throughout.
|
|
175
|
+
*
|
|
176
|
+
* Which is also why a caller must NOT try to reclaim it by calling
|
|
177
|
+
* `destroySharedWorkerPool()` on an idle timer of its own: a destroyed pool
|
|
178
|
+
* throws out of `decompressBlocks`, so every open `BamFile` still holding
|
|
179
|
+
* one would fail its next read rather than fall back to inflating in
|
|
180
|
+
* process. Reclaiming is the pool's job, not the consumer's.
|
|
167
181
|
*/
|
|
168
182
|
bgzfWorkerPool?: BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined;
|
|
169
183
|
/**
|
package/esm/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
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1
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+
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QAAQ,EAAE,CAAC,CAAC,CAAA;QACpE,OAAO,aAAa,CAAC,IAAI,EAAE,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,kBAAkB,CAAC,KAAY,EAAE,IAAc;QACnD,yEAAyE;QACzE,6EAA6E;QAC7E,0EAA0E;QAC1E,uEAAuE;QACvE,0CAA0C;QAC1C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC7B,KAAK,CAAC,WAAW,EAAE,EACnB,KAAK,CAAC,IAAI,CAAC,aAAa,EACxB;YACE,MAAM,EAAE,IAAI,CAAC,MAAM;SACpB,CACF,CAAA;QACD,0EAA0E;QAC1E,oEAAoE;QACpE,2EAA2E;QAC3E,yEAAyE;QACzE,4EAA4E;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,oEAAoE;QACpE,EAAE;QACF,uEAAuE;QACvE,sEAAsE;QACtE,2EAA2E;QAC3E,sEAAsE;QACtE,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAE3B,wEAAwE;QACxE,qEAAqE;QACrE,6CAA6C;QAC7C,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QACtC,MAAM,EACJ,MAAM,EAAE,IAAI,EACZ,UAAU,EACV,UAAU,GACX,GAAG,MAAM,eAAe,CAAC,GAAG,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;QAC3C,OAAO;YACL,QAAQ,EAAE,IAAI,CAAC,eAAe,CAAC,IAAI,EAAE,UAAU,EAAE,UAAU,EAAE,KAAK,CAAC;YACnE,KAAK,EAAE,IAAI,CAAC,UAAU;SACvB,CAAA;IACH,CAAC;IAED,0EAA0E;IAC1E,8EAA8E;IAC9E,8EAA8E;IAC9E,sEAAsE;IACtE,uCAAuC;IACvC,eAAe,CACb,EAAc,EACd,UAA6B,EAC7B,UAA6B,EAC7B,KAAY;QAEZ,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,MAAM,IAAI,GAAG,EAAS,CAAA;QACtB,IAAI,GAAG,GAAG,CAAC,CAAA;QAEX,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,CAAC,MAAM,EAAE,EAAE,CAAC,UAAU,EAAE,EAAE,CAAC,UAAU,CAAC,CAAA;QACtE,MAAM,aAAa,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAC3C,MAAM,aAAa,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAE3C,OAAO,UAAU,GAAG,CAAC,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC;YAClC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;YACrD,MAAM,QAAQ,GAAG,UAAU,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,CAAA;YAE/C,IAAI,aAAa,EAAE,CAAC;gBAClB,MAAM,MAAM,GAAG,UAAU,GAAG,KAAK,CAAC,IAAI,CAAC,YAAY,CAAA;gBACnD,OAAO,GAAG,GAAG,UAAU,CAAC,MAAM,IAAI,MAAM,IAAI,UAAU,CAAC,GAAG,CAAE,EAAE,CAAC;oBAC7D,GAAG,EAAE,CAAA;gBACP,CAAC;YACH,CAAC;YAED,IAAI,QAAQ,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC;gBACzB,MAAM,OAAO,GAAG,IAAI,IAAI,CAAC,WAAW,CAClC,EAAE,EACF,UAAU,EACV,QAAQ,EACR,aAAa;oBACX,CAAC,CAAC,UAAU,CAAC,GAAG,CAAE,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;wBACzB,CAAC,UAAU,GAAG,UAAU,CAAC,GAAG,CAAE,CAAC;wBAC/B,KAAK,CAAC,IAAI,CAAC,YAAY;wBACvB,CAAC;oBACL,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,QAAQ,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC,KAAK,CAAC,EAClD,QAAQ,CACT,CAAA;gBAED,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACpB,CAAC;YAED,UAAU,GAAG,QAAQ,GAAG,CAAC,CAAA;QAC3B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,IAAe;QAC9C,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QAChD,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS;YACvC,CAAC,CAAC,KAAK;YACP,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;IACjC,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,IAAe;QAC9C,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QAChD,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;IAC7E,CAAC;IAED,KAAK,CAAC,QAAQ,CAAC,OAAe,EAAE,KAAc,EAAE,GAAY;QAC1D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAA;QAC1C,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS;YACvC,CAAC,CAAC,EAAE;YACJ,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,OAAe,EACf,KAAa,EACb,GAAW,EACX,IAAe;QAEf,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QAChD,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS;YACvC,CAAC,CAAC,EAAE;YACJ,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,iBAAiB;QACf,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,CAAA;IAChC,CAAC;IAED,KAAK,CAAC,wBAAwB,CAC5B,OAA0D,EAC1D,IAAe;QAEf,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YAChB,OAAO,CAAC,CAAA;QACV,CAAC;QACD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACjC,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;YAC1C,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,GAAG,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QAC3E,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,KAAK,CAAC,wBAAwB,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAC1D,CAAC;CACF"}
|
package/esm/index.d.ts
CHANGED
|
@@ -4,7 +4,7 @@ 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 { MISMATCH_DELETION, MISMATCH_HARD_CLIP, MISMATCH_INSERTION, MISMATCH_REF_SKIP, MISMATCH_SOFT_CLIP, MISMATCH_SUBST, forEachMismatchNumeric, } from './mismatches.ts';
|
|
7
|
-
export { packReference } from './reference.ts';
|
|
7
|
+
export { CHAR_CODE_FROM_NIBBLE, packReference, referenceNibble, } from './reference.ts';
|
|
8
8
|
export type { NumericCigar } from './record.ts';
|
|
9
9
|
export type { BamRecordClass, BamRecordLike, ReferenceSequenceFetcher, } from './bamFile.ts';
|
|
10
10
|
export type { Mismatch, MismatchCallback, MismatchOptions, } from './mismatches.ts';
|
package/esm/index.js
CHANGED
|
@@ -8,5 +8,8 @@ export { default as HtsgetFile } from "./htsget.js";
|
|
|
8
8
|
// arrays without a record around them — a SAM parser, or a worker that was
|
|
9
9
|
// posted the typed arrays.
|
|
10
10
|
export { MISMATCH_DELETION, MISMATCH_HARD_CLIP, MISMATCH_INSERTION, MISMATCH_REF_SKIP, MISMATCH_SOFT_CLIP, MISMATCH_SUBST, forEachMismatchNumeric, } from "./mismatches.js";
|
|
11
|
-
|
|
11
|
+
// `referenceNibble` and `CHAR_CODE_FROM_NIBBLE` are what read a base back out
|
|
12
|
+
// of a packed region — a consumer that holds one otherwise has no way to see
|
|
13
|
+
// what is in it, which makes a binding untestable from the outside.
|
|
14
|
+
export { CHAR_CODE_FROM_NIBBLE, packReference, referenceNibble, } from "./reference.js";
|
|
12
15
|
//# sourceMappingURL=index.js.map
|
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,EACL,6BAA6B,EAC7B,uBAAuB,EACvB,OAAO,IAAI,OAAO,GACnB,MAAM,cAAc,CAAA;AACrB,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;AAEnD,0EAA0E;AAC1E,+EAA+E;AAC/E,2EAA2E;AAC3E,2BAA2B;AAC3B,OAAO,EACL,iBAAiB,EACjB,kBAAkB,EAClB,kBAAkB,EAClB,iBAAiB,EACjB,kBAAkB,EAClB,cAAc,EACd,sBAAsB,GACvB,MAAM,iBAAiB,CAAA;AACxB,OAAO,
|
|
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,EACL,6BAA6B,EAC7B,uBAAuB,EACvB,OAAO,IAAI,OAAO,GACnB,MAAM,cAAc,CAAA;AACrB,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;AAEnD,0EAA0E;AAC1E,+EAA+E;AAC/E,2EAA2E;AAC3E,2BAA2B;AAC3B,OAAO,EACL,iBAAiB,EACjB,kBAAkB,EAClB,kBAAkB,EAClB,iBAAiB,EACjB,kBAAkB,EAClB,cAAc,EACd,sBAAsB,GACvB,MAAM,iBAAiB,CAAA;AACxB,8EAA8E;AAC9E,6EAA6E;AAC7E,oEAAoE;AACpE,OAAO,EACL,qBAAqB,EACrB,aAAa,EACb,eAAe,GAChB,MAAM,gBAAgB,CAAA"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/bam",
|
|
3
|
-
"version": "8.
|
|
3
|
+
"version": "8.8.1",
|
|
4
4
|
"packageManager": "pnpm@11.15.1",
|
|
5
5
|
"description": "Parser for BAM and BAM index (bai) files",
|
|
6
6
|
"license": "MIT",
|
|
@@ -51,7 +51,7 @@
|
|
|
51
51
|
"genomics"
|
|
52
52
|
],
|
|
53
53
|
"dependencies": {
|
|
54
|
-
"@gmod/bgzf-filehandle": "^6.
|
|
54
|
+
"@gmod/bgzf-filehandle": "^6.6.0",
|
|
55
55
|
"@gmod/shared-read-cache": "^1.5.1",
|
|
56
56
|
"@jbrowse/quick-lru": "^7.3.5",
|
|
57
57
|
"crc": "^4.3.2",
|
package/src/bamFile.ts
CHANGED
|
@@ -318,6 +318,20 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
318
318
|
* has long since resolved. `undefined` (which is what that helper gives
|
|
319
319
|
* back under node, or anywhere Workers cannot be created) keeps the
|
|
320
320
|
* in-process path, so this is safe to pass unconditionally.
|
|
321
|
+
*
|
|
322
|
+
* **Holding a pool for the life of this object is fine, and deliberately
|
|
323
|
+
* so.** It is stored here and awaited once per chunk read, which used to
|
|
324
|
+
* mean four workers and their grow-only wasm heaps stayed up from the first
|
|
325
|
+
* query until the page went away. As of `@gmod/bgzf-filehandle` 6.6.0 a
|
|
326
|
+
* pool reaps its own workers after 3 minutes idle and spawns a fresh set on
|
|
327
|
+
* the next call, and that is invisible from here — the pool object stays
|
|
328
|
+
* valid throughout.
|
|
329
|
+
*
|
|
330
|
+
* Which is also why a caller must NOT try to reclaim it by calling
|
|
331
|
+
* `destroySharedWorkerPool()` on an idle timer of its own: a destroyed pool
|
|
332
|
+
* throws out of `decompressBlocks`, so every open `BamFile` still holding
|
|
333
|
+
* one would fail its next read rather than fall back to inflating in
|
|
334
|
+
* process. Reclaiming is the pool's job, not the consumer's.
|
|
321
335
|
*/
|
|
322
336
|
bgzfWorkerPool?:
|
|
323
337
|
BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined
|
package/src/index.ts
CHANGED
|
@@ -21,7 +21,14 @@ export {
|
|
|
21
21
|
MISMATCH_SUBST,
|
|
22
22
|
forEachMismatchNumeric,
|
|
23
23
|
} from './mismatches.ts'
|
|
24
|
-
|
|
24
|
+
// `referenceNibble` and `CHAR_CODE_FROM_NIBBLE` are what read a base back out
|
|
25
|
+
// of a packed region — a consumer that holds one otherwise has no way to see
|
|
26
|
+
// what is in it, which makes a binding untestable from the outside.
|
|
27
|
+
export {
|
|
28
|
+
CHAR_CODE_FROM_NIBBLE,
|
|
29
|
+
packReference,
|
|
30
|
+
referenceNibble,
|
|
31
|
+
} from './reference.ts'
|
|
25
32
|
|
|
26
33
|
export type { NumericCigar } from './record.ts'
|
|
27
34
|
export type {
|