@gmod/bam 5.0.1 → 5.0.4
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/CHANGELOG.md +12 -0
- package/dist/bamFile.js +5 -4
- package/dist/bamFile.js.map +1 -1
- package/dist/util.d.ts +4 -3
- package/dist/util.js +6 -8
- package/dist/util.js.map +1 -1
- package/esm/bamFile.js +5 -4
- package/esm/bamFile.js.map +1 -1
- package/esm/util.d.ts +4 -3
- package/esm/util.js +6 -5
- package/esm/util.js.map +1 -1
- package/package.json +2 -6
- package/src/bamFile.ts +5 -4
- package/src/util.ts +6 -8
package/CHANGELOG.md
CHANGED
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@@ -1,3 +1,15 @@
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1
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## [5.0.4](https://github.com/GMOD/bam-js/compare/v5.0.2...v5.0.4) (2024-12-18)
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## [5.0.3](https://github.com/GMOD/bam-js/compare/v5.0.2...v5.0.3) (2024-12-18)
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## [5.0.2](https://github.com/GMOD/bam-js/compare/v5.0.1...v5.0.2) (2024-12-17)
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## [5.0.1](https://github.com/GMOD/bam-js/compare/v5.0.0...v5.0.1) (2024-12-12)
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package/dist/bamFile.js
CHANGED
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@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.BAM_MAGIC = void 0;
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-
const crc32_1 = __importDefault(require("crc/crc32"));
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const crc32_1 = __importDefault(require("crc/calculators/crc32"));
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const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
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const generic_filehandle2_1 = require("generic-filehandle2");
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const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
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@@ -344,9 +344,10 @@ class BamFile {
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(blockStart - dpositions[pos]) +
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chunk.minv.dataPosition +
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1
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: //
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//
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-
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: // this shift >>> 0 is equivalent to crc32(b).unsigned but uses the
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// internal calculator of crc32 to avoid accidentally importing buffer
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// https://github.com/alexgorbatchev/crc/blob/31fc3853e417b5fb5ec83335428805842575f699/src/define_crc.ts#L5
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(0, crc32_1.default)(ba.subarray(blockStart, blockEnd)) >>> 0,
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});
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sink.push(feature);
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if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {
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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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|
package/dist/util.d.ts
CHANGED
|
@@ -3,9 +3,10 @@ import VirtualOffset from './virtualOffset';
|
|
|
3
3
|
export declare function timeout(ms: number): Promise<unknown>;
|
|
4
4
|
/**
|
|
5
5
|
* Properly check if the given AbortSignal is aborted.
|
|
6
|
-
*
|
|
7
|
-
*
|
|
8
|
-
* with a `code` attribute
|
|
6
|
+
*
|
|
7
|
+
* Per the standard, if the signal reads as aborted, this function throws
|
|
8
|
+
* either a DOMException AbortError, or a regular error with a `code` attribute
|
|
9
|
+
* set to `ERR_ABORTED`.
|
|
9
10
|
*
|
|
10
11
|
* For convenience, passing `undefined` is a no-op
|
|
11
12
|
*
|
package/dist/util.js
CHANGED
|
@@ -1,7 +1,4 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
3
|
-
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
|
-
};
|
|
5
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
3
|
exports.timeout = timeout;
|
|
7
4
|
exports.checkAbortSignal = checkAbortSignal;
|
|
@@ -14,15 +11,16 @@ exports.findFirstData = findFirstData;
|
|
|
14
11
|
exports.parseNameBytes = parseNameBytes;
|
|
15
12
|
exports.sum = sum;
|
|
16
13
|
exports.concatUint8Array = concatUint8Array;
|
|
17
|
-
const
|
|
14
|
+
const longfn_1 = require("longfn");
|
|
18
15
|
function timeout(ms) {
|
|
19
16
|
return new Promise(resolve => setTimeout(resolve, ms));
|
|
20
17
|
}
|
|
21
18
|
/**
|
|
22
19
|
* Properly check if the given AbortSignal is aborted.
|
|
23
|
-
*
|
|
24
|
-
*
|
|
25
|
-
* with a `code` attribute
|
|
20
|
+
*
|
|
21
|
+
* Per the standard, if the signal reads as aborted, this function throws
|
|
22
|
+
* either a DOMException AbortError, or a regular error with a `code` attribute
|
|
23
|
+
* set to `ERR_ABORTED`.
|
|
26
24
|
*
|
|
27
25
|
* For convenience, passing `undefined` is a no-op
|
|
28
26
|
*
|
|
@@ -96,7 +94,7 @@ function optimizeChunks(chunks, lowest) {
|
|
|
96
94
|
}
|
|
97
95
|
function parsePseudoBin(bytes, offset) {
|
|
98
96
|
return {
|
|
99
|
-
lineCount:
|
|
97
|
+
lineCount: (0, longfn_1.toNumber)((0, longfn_1.fromBytesLE)(bytes.subarray(offset, offset + 8), true)),
|
|
100
98
|
};
|
|
101
99
|
}
|
|
102
100
|
function findFirstData(firstDataLine, virtualOffset) {
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAIA,0BAEC;AAcD,4CAgBC;AAQD,0CAGC;AAED,wCAKC;AAaD,4BAEC;AAED,wCAgCC;AAED,wCAIC;AAED,sCASC;AAED,wCAwBC;AAED,kBAMC;AACD,4CAQC;AAnKD,mCAA8C;AAI9C,SAAgB,OAAO,CAAC,EAAU;IAChC,OAAO,IAAI,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAED;;;;;;;;;;;GAWG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;YAC9B,YAAY;YACZ,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACI,KAAK,UAAU,eAAe,CAAC,MAAoB;IACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;IACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;AAC1B,CAAC;AAED,SAAgB,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AAaD,SAAgB,QAAQ,CAAC,MAA8B,EAAE;IACvD,OAAO,SAAS,IAAI,GAAG,CAAC,CAAC,CAAE,EAAE,MAAM,EAAE,GAAG,EAAe,CAAC,CAAC,CAAC,GAAG,CAAA;AAC/D,CAAC;AAED,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAA4B,CAAA;IAEhC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;IAED,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACrB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;YAChD,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;gBAC5B,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE,CAAC;oBACrC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC7C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;oBAC7B,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,SAAgB,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO;QACL,SAAS,EAAE,IAAA,iBAAQ,EAAC,IAAA,oBAAW,EAAC,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,MAAM,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC;KAC3E,CAAA;AACH,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,SAAgB,cAAc,CAC5B,UAAsB,EACtB,eAAwC,CAAC,CAAC,EAAE,CAAC,CAAC;IAE9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,MAAM,WAAW,GAA2B,EAAE,CAAA;IAC9C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;gBACtB,IAAI,OAAO,GAAG,EAAE,CAAA;gBAChB,KAAK,IAAI,CAAC,GAAG,aAAa,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;oBACvC,OAAO,IAAI,MAAM,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA;gBAC/C,CAAC;gBACD,OAAO,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;gBAC/B,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,IAAI,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AAED,SAAgB,GAAG,CAAC,KAAmB;IACrC,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,MAAM,KAAK,IAAI,KAAK,EAAE,CAAC;QAC1B,GAAG,IAAI,KAAK,CAAC,MAAM,CAAA;IACrB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AACD,SAAgB,gBAAgB,CAAC,IAAkB;IACjD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAA;IAC7C,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"}
|
package/esm/bamFile.js
CHANGED
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import crc32 from 'crc/crc32';
|
|
1
|
+
import crc32 from 'crc/calculators/crc32';
|
|
2
2
|
import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
|
|
3
3
|
import { LocalFile, RemoteFile } from 'generic-filehandle2';
|
|
4
4
|
import AbortablePromiseCache from '@gmod/abortable-promise-cache';
|
|
@@ -338,9 +338,10 @@ export default class BamFile {
|
|
|
338
338
|
(blockStart - dpositions[pos]) +
|
|
339
339
|
chunk.minv.dataPosition +
|
|
340
340
|
1
|
|
341
|
-
: //
|
|
342
|
-
//
|
|
343
|
-
|
|
341
|
+
: // this shift >>> 0 is equivalent to crc32(b).unsigned but uses the
|
|
342
|
+
// internal calculator of crc32 to avoid accidentally importing buffer
|
|
343
|
+
// https://github.com/alexgorbatchev/crc/blob/31fc3853e417b5fb5ec83335428805842575f699/src/define_crc.ts#L5
|
|
344
|
+
crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
|
|
344
345
|
});
|
|
345
346
|
sink.push(feature);
|
|
346
347
|
if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {
|
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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|
package/esm/util.d.ts
CHANGED
|
@@ -3,9 +3,10 @@ import VirtualOffset from './virtualOffset';
|
|
|
3
3
|
export declare function timeout(ms: number): Promise<unknown>;
|
|
4
4
|
/**
|
|
5
5
|
* Properly check if the given AbortSignal is aborted.
|
|
6
|
-
*
|
|
7
|
-
*
|
|
8
|
-
* with a `code` attribute
|
|
6
|
+
*
|
|
7
|
+
* Per the standard, if the signal reads as aborted, this function throws
|
|
8
|
+
* either a DOMException AbortError, or a regular error with a `code` attribute
|
|
9
|
+
* set to `ERR_ABORTED`.
|
|
9
10
|
*
|
|
10
11
|
* For convenience, passing `undefined` is a no-op
|
|
11
12
|
*
|
package/esm/util.js
CHANGED
|
@@ -1,12 +1,13 @@
|
|
|
1
|
-
import
|
|
1
|
+
import { fromBytesLE, toNumber } from 'longfn';
|
|
2
2
|
export function timeout(ms) {
|
|
3
3
|
return new Promise(resolve => setTimeout(resolve, ms));
|
|
4
4
|
}
|
|
5
5
|
/**
|
|
6
6
|
* Properly check if the given AbortSignal is aborted.
|
|
7
|
-
*
|
|
8
|
-
*
|
|
9
|
-
* with a `code` attribute
|
|
7
|
+
*
|
|
8
|
+
* Per the standard, if the signal reads as aborted, this function throws
|
|
9
|
+
* either a DOMException AbortError, or a regular error with a `code` attribute
|
|
10
|
+
* set to `ERR_ABORTED`.
|
|
10
11
|
*
|
|
11
12
|
* For convenience, passing `undefined` is a no-op
|
|
12
13
|
*
|
|
@@ -80,7 +81,7 @@ export function optimizeChunks(chunks, lowest) {
|
|
|
80
81
|
}
|
|
81
82
|
export function parsePseudoBin(bytes, offset) {
|
|
82
83
|
return {
|
|
83
|
-
lineCount:
|
|
84
|
+
lineCount: toNumber(fromBytesLE(bytes.subarray(offset, offset + 8), true)),
|
|
84
85
|
};
|
|
85
86
|
}
|
|
86
87
|
export function findFirstData(firstDataLine, virtualOffset) {
|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,QAAQ,CAAA;AAI9C,MAAM,UAAU,OAAO,CAAC,EAAU;IAChC,OAAO,IAAI,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;YAC9B,YAAY;YACZ,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,eAAe,CAAC,MAAoB;IACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;IACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AAaD,MAAM,UAAU,QAAQ,CAAC,MAA8B,EAAE;IACvD,OAAO,SAAS,IAAI,GAAG,CAAC,CAAC,CAAE,EAAE,MAAM,EAAE,GAAG,EAAe,CAAC,CAAC,CAAC,GAAG,CAAA;AAC/D,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAA4B,CAAA;IAEhC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;IAED,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACrB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;YAChD,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;gBAC5B,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE,CAAC;oBACrC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC7C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;oBAC7B,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO;QACL,SAAS,EAAE,QAAQ,CAAC,WAAW,CAAC,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,MAAM,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC;KAC3E,CAAA;AACH,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,MAAM,UAAU,cAAc,CAC5B,UAAsB,EACtB,eAAwC,CAAC,CAAC,EAAE,CAAC,CAAC;IAE9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,MAAM,WAAW,GAA2B,EAAE,CAAA;IAC9C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;gBACtB,IAAI,OAAO,GAAG,EAAE,CAAA;gBAChB,KAAK,IAAI,CAAC,GAAG,aAAa,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;oBACvC,OAAO,IAAI,MAAM,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA;gBAC/C,CAAC;gBACD,OAAO,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;gBAC/B,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,IAAI,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AAED,MAAM,UAAU,GAAG,CAAC,KAAmB;IACrC,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,MAAM,KAAK,IAAI,KAAK,EAAE,CAAC;QAC1B,GAAG,IAAI,KAAK,CAAC,MAAM,CAAA;IACrB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AACD,MAAM,UAAU,gBAAgB,CAAC,IAAkB;IACjD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAA;IAC7C,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"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/bam",
|
|
3
|
-
"version": "5.0.
|
|
3
|
+
"version": "5.0.4",
|
|
4
4
|
"description": "Parser for BAM and BAM index (bai) files",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/bam-js",
|
|
@@ -42,19 +42,15 @@
|
|
|
42
42
|
"@gmod/bgzf-filehandle": "^2.0.1",
|
|
43
43
|
"crc": "^4.3.2",
|
|
44
44
|
"generic-filehandle2": "^1.0.0",
|
|
45
|
-
"
|
|
45
|
+
"longfn": "^1.3.1",
|
|
46
46
|
"quick-lru": "^4.0.0"
|
|
47
47
|
},
|
|
48
48
|
"devDependencies": {
|
|
49
|
-
"@types/long": "^4.0.0",
|
|
50
49
|
"@types/node": "^20.11.19",
|
|
51
50
|
"@typescript-eslint/eslint-plugin": "^8.1.0",
|
|
52
51
|
"@typescript-eslint/parser": "^8.1.0",
|
|
53
52
|
"@vitest/coverage-v8": "^2.0.5",
|
|
54
|
-
"buffer": "^6.0.3",
|
|
55
53
|
"eslint": "^9.9.0",
|
|
56
|
-
"eslint-config-prettier": "^9.1.0",
|
|
57
|
-
"eslint-plugin-prettier": "^5.1.3",
|
|
58
54
|
"eslint-plugin-unicorn": "^56.0.0",
|
|
59
55
|
"prettier": "^3.3.3",
|
|
60
56
|
"rimraf": "^6.0.1",
|
package/src/bamFile.ts
CHANGED
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import crc32 from 'crc/crc32'
|
|
1
|
+
import crc32 from 'crc/calculators/crc32'
|
|
2
2
|
import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
|
|
3
3
|
import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle2'
|
|
4
4
|
import AbortablePromiseCache from '@gmod/abortable-promise-cache'
|
|
@@ -451,9 +451,10 @@ export default class BamFile {
|
|
|
451
451
|
(blockStart - dpositions[pos]) +
|
|
452
452
|
chunk.minv.dataPosition +
|
|
453
453
|
1
|
|
454
|
-
: //
|
|
455
|
-
//
|
|
456
|
-
|
|
454
|
+
: // this shift >>> 0 is equivalent to crc32(b).unsigned but uses the
|
|
455
|
+
// internal calculator of crc32 to avoid accidentally importing buffer
|
|
456
|
+
// https://github.com/alexgorbatchev/crc/blob/31fc3853e417b5fb5ec83335428805842575f699/src/define_crc.ts#L5
|
|
457
|
+
crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
|
|
457
458
|
})
|
|
458
459
|
|
|
459
460
|
sink.push(feature)
|
package/src/util.ts
CHANGED
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import
|
|
1
|
+
import { fromBytesLE, toNumber } from 'longfn'
|
|
2
2
|
import Chunk from './chunk'
|
|
3
3
|
import VirtualOffset from './virtualOffset'
|
|
4
4
|
|
|
@@ -8,9 +8,10 @@ export function timeout(ms: number) {
|
|
|
8
8
|
|
|
9
9
|
/**
|
|
10
10
|
* Properly check if the given AbortSignal is aborted.
|
|
11
|
-
*
|
|
12
|
-
*
|
|
13
|
-
* with a `code` attribute
|
|
11
|
+
*
|
|
12
|
+
* Per the standard, if the signal reads as aborted, this function throws
|
|
13
|
+
* either a DOMException AbortError, or a regular error with a `code` attribute
|
|
14
|
+
* set to `ERR_ABORTED`.
|
|
14
15
|
*
|
|
15
16
|
* For convenience, passing `undefined` is a no-op
|
|
16
17
|
*
|
|
@@ -104,10 +105,7 @@ export function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset) {
|
|
|
104
105
|
|
|
105
106
|
export function parsePseudoBin(bytes: Uint8Array, offset: number) {
|
|
106
107
|
return {
|
|
107
|
-
lineCount:
|
|
108
|
-
Array.prototype.slice.call(bytes, offset, offset + 8),
|
|
109
|
-
true,
|
|
110
|
-
).toNumber(),
|
|
108
|
+
lineCount: toNumber(fromBytesLE(bytes.subarray(offset, offset + 8), true)),
|
|
111
109
|
}
|
|
112
110
|
}
|
|
113
111
|
|