@gmod/bam 7.1.13 → 7.1.15
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 +5 -1
- package/dist/bai.js +1 -1
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +1 -1
- package/dist/bamFile.js +1 -1
- package/dist/bamFile.js.map +1 -1
- package/dist/csi.js +1 -1
- package/dist/csi.js.map +1 -1
- package/esm/bai.js +1 -1
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +1 -1
- package/esm/bamFile.js +1 -1
- package/esm/bamFile.js.map +1 -1
- package/esm/csi.js +1 -1
- package/esm/csi.js.map +1 -1
- package/package.json +6 -6
- package/src/bai.ts +1 -1
- package/src/bamFile.ts +1 -1
- package/src/csi.ts +1 -1
package/CHANGELOG.md
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@@ -1,6 +1,10 @@
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## [7.1.
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## [7.1.15](https://github.com/GMOD/bam-js/compare/v7.1.14...v7.1.15) (2025-12-17)
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## [7.1.14](https://github.com/GMOD/bam-js/compare/v7.1.13...v7.1.14) (2025-12-17)
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## [7.1.13](https://github.com/GMOD/bam-js/compare/v7.1.12...v7.1.13) (2025-12-17)
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## [7.1.12](https://github.com/GMOD/bam-js/compare/v7.1.11...v7.1.12) (2025-12-17)
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package/dist/bai.js
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@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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const quick_lru_1 = __importDefault(require("quick-lru"));
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const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
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const chunk_ts_1 = __importDefault(require("./chunk.js"));
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const indexFile_ts_1 = __importDefault(require("./indexFile.js"));
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const util_ts_1 = require("./util.js");
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package/dist/bai.js.map
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@@ -1 +1 @@
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1
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{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;AAAA,
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{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;AAAA,mEAAyC;AAEzC,0DAA8B;AAC9B,kEAAsC;AACtC,uCAKkB;AAClB,yDAA6D;AAE7D,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,GAAG,QAAQ,CAAA;AACtC,CAAC;AAQD,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAGxC,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,KAAgB;QAC3B,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAA;QAC9C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,0BAA0B;QAC1B,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC9C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC3C,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,aAAwC,CAAA;QAE5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAE9C,IAAI,IAAI,CAAC,CAAA;YAET,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;oBACX,CAAC;gBACH,CAAC;YACH,CAAC;YAED,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,mEAAmE;YACnE,qEAAqE;YACrE,OAAO;YACP,MAAM,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,MAAM,MAAM,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACrC,IAAI,IAAI,CAAC,CAAA;gBACT,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,MAAM,CAAC,CAAA;gBACpD,WAAW,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;YACzB,CAAC;QACH,CAAC;QACD,MAAM,YAAY,GAAG,IAAI,mBAAQ,CAAwC;YACvE,OAAO,EAAE,CAAC;SACX,CAAC,CAAA;QAEF,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,KAAK,CAAA;YAET,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAE5C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACxC,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;oBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBAC/C,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,mEAAmE;YACnE,qEAAqE;YACrE,OAAO;YACP,MAAM,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,MAAM,MAAM,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACrC,IAAI,IAAI,CAAC,CAAA;gBACT,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,MAAM,CAAC,CAAA;gBACpD,WAAW,CAAC,CAAC,CAAC,GAAG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package/dist/bamFile.js
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exports.BAM_MAGIC = void 0;
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const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
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const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
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const crc32_1 = __importDefault(require("crc/calculators/crc32"));
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const generic_filehandle2_1 = require("generic-filehandle2");
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const quick_lru_1 = __importDefault(require("quick-lru"));
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const bai_ts_1 = __importDefault(require("./bai.js"));
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const csi_ts_1 = __importDefault(require("./csi.js"));
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const nullFilehandle_ts_1 = __importDefault(require("./nullFilehandle.js"));
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package/dist/bamFile.js.map
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1
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+
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|
package/dist/csi.js
CHANGED
|
@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
7
|
-
const quick_lru_1 = __importDefault(require("quick-lru"));
|
|
7
|
+
const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
|
|
8
8
|
const chunk_ts_1 = __importDefault(require("./chunk.js"));
|
|
9
9
|
const indexFile_ts_1 = __importDefault(require("./indexFile.js"));
|
|
10
10
|
const util_ts_1 = require("./util.js");
|
package/dist/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAC7C,
|
|
1
|
+
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+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,oBAAoB,CAAA;AAEzC,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EAEL,aAAa,EACb,cAAc,EACd,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAiB,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAE7D,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,GAAG,QAAQ,CAAA;AACtC,CAAC;AAQD,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAGxC,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,KAAgB;QAC3B,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAA;QAC9C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,0BAA0B;QAC1B,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC9C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC3C,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,aAAwC,CAAA;QAE5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAE9C,IAAI,IAAI,CAAC,CAAA;YAET,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;oBACX,CAAC;gBACH,CAAC;YACH,CAAC;YAED,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,mEAAmE;YACnE,qEAAqE;YACrE,OAAO;YACP,MAAM,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,MAAM,MAAM,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACrC,IAAI,IAAI,CAAC,CAAA;gBACT,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,MAAM,CAAC,CAAA;gBACpD,WAAW,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;YACzB,CAAC;QACH,CAAC;QACD,MAAM,YAAY,GAAG,IAAI,QAAQ,CAAwC;YACvE,OAAO,EAAE,CAAC;SACX,CAAC,CAAA;QAEF,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,KAAK,CAAA;YAET,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAE5C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,GAAG,cAAc,CAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACxC,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;oBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBAC/C,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,mEAAmE;YACnE,qEAAqE;YACrE,OAAO;YACP,MAAM,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,MAAM,MAAM,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACrC,IAAI,IA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|
package/esm/bamFile.d.ts
CHANGED
package/esm/bamFile.js
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
|
|
2
|
+
import QuickLRU from '@jbrowse/quick-lru';
|
|
2
3
|
import crc32 from 'crc/calculators/crc32';
|
|
3
4
|
import { LocalFile, RemoteFile } from 'generic-filehandle2';
|
|
4
|
-
import QuickLRU from 'quick-lru';
|
|
5
5
|
import BAI from "./bai.js";
|
|
6
6
|
import CSI from "./csi.js";
|
|
7
7
|
import NullFilehandle from "./nullFilehandle.js";
|
package/esm/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/esm/csi.js
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { unzip } from '@gmod/bgzf-filehandle';
|
|
2
|
-
import QuickLRU from 'quick-lru';
|
|
2
|
+
import QuickLRU from '@jbrowse/quick-lru';
|
|
3
3
|
import Chunk from "./chunk.js";
|
|
4
4
|
import IndexFile from "./indexFile.js";
|
|
5
5
|
import { findFirstData, optimizeChunks, parseNameBytes, parsePseudoBin, } from "./util.js";
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,QAAQ,MAAM,
|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/bam",
|
|
3
|
-
"version": "7.1.
|
|
3
|
+
"version": "7.1.15",
|
|
4
4
|
"description": "Parser for BAM and BAM index (bai) files",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/bam-js",
|
|
@@ -50,14 +50,14 @@
|
|
|
50
50
|
"genomics"
|
|
51
51
|
],
|
|
52
52
|
"dependencies": {
|
|
53
|
-
"@gmod/bgzf-filehandle": "^6.0.
|
|
53
|
+
"@gmod/bgzf-filehandle": "^6.0.9",
|
|
54
|
+
"@jbrowse/quick-lru": "^7.3.5",
|
|
54
55
|
"crc": "^4.3.2",
|
|
55
|
-
"generic-filehandle2": "^2.0.16"
|
|
56
|
-
"quick-lru": "^4.0.0"
|
|
56
|
+
"generic-filehandle2": "^2.0.16"
|
|
57
57
|
},
|
|
58
58
|
"devDependencies": {
|
|
59
59
|
"@types/node": "^24.10.0",
|
|
60
|
-
"@vitest/coverage-v8": "^4.0.
|
|
60
|
+
"@vitest/coverage-v8": "^4.0.16",
|
|
61
61
|
"eslint": "^9.9.0",
|
|
62
62
|
"eslint-plugin-import": "^2.31.0",
|
|
63
63
|
"eslint-plugin-unicorn": "^62.0.0",
|
|
@@ -66,7 +66,7 @@
|
|
|
66
66
|
"standard-changelog": "^7.0.1",
|
|
67
67
|
"typescript": "^5.0.4",
|
|
68
68
|
"typescript-eslint": "^8.49.0",
|
|
69
|
-
"vitest": "^4.0.
|
|
69
|
+
"vitest": "^4.0.16"
|
|
70
70
|
},
|
|
71
71
|
"publishConfig": {
|
|
72
72
|
"access": "public"
|
package/src/bai.ts
CHANGED
package/src/bamFile.ts
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
|
|
2
|
+
import QuickLRU from '@jbrowse/quick-lru'
|
|
2
3
|
import crc32 from 'crc/calculators/crc32'
|
|
3
4
|
import { LocalFile, RemoteFile } from 'generic-filehandle2'
|
|
4
|
-
import QuickLRU from 'quick-lru'
|
|
5
5
|
|
|
6
6
|
import BAI from './bai.ts'
|
|
7
7
|
import Chunk from './chunk.ts'
|
package/src/csi.ts
CHANGED