@gmod/bam 7.1.12 → 7.1.14
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 +6 -2
- package/dist/bai.js +1 -1
- package/dist/bai.js.map +1 -1
- package/dist/csi.js +1 -1
- package/dist/csi.js.map +1 -1
- package/dist/record.js +5 -10
- package/dist/record.js.map +1 -1
- package/esm/bai.js +1 -1
- package/esm/bai.js.map +1 -1
- package/esm/csi.js +1 -1
- package/esm/csi.js.map +1 -1
- package/esm/record.js +6 -11
- package/esm/record.js.map +1 -1
- package/package.json +6 -6
- package/src/bai.ts +1 -1
- package/src/csi.ts +1 -1
- package/src/record.ts +6 -17
package/CHANGELOG.md
CHANGED
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@@ -1,10 +1,14 @@
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-
## [7.1.
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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.
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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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## [7.1.11](https://github.com/GMOD/bam-js/compare/v7.1.10...v7.1.11) (2025-12-16)
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## [7.1.10](https://github.com/GMOD/bam-js/compare/v7.1.9...v7.1.10) (2025-12-15)
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14
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package/dist/bai.js
CHANGED
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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
CHANGED
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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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1
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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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const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
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package/dist/csi.js.map
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{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAC7C,
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|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAC7C,mEAAyC;AAEzC,0DAA8B;AAC9B,kEAAsC;AACtC,uCAKkB;AAClB,yDAA6D;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAA1C;;QACU,iBAAY,GAAG,CAAC,CAAA;QAChB,UAAK,GAAG,CAAC,CAAA;QACT,aAAQ,GAAG,CAAC,CAAA;IAwPtB,CAAC;IApPC,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,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACpD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GACV,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EACnC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACpB,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,OAAO;YACL,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW;YACX,GAAG,IAAA,wBAAc,EACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAA8B;QACzC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACnD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,IAAI,UAAU,CAAA;QACd,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAEzC,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;YAC1C,oDAAoD;QACtD,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACtE,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,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;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,IAAI,IAAI,CAAC,CAAA;oBACT,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,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;wBACT,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;oBACjD,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,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,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,cAAc,CAAA;YAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,cAAc,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACjD,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;oBACpE,IAAI,IAAI,CAAC,CAAA;oBACT,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,IAAI,CAAC,EAAE,CAAC;wBACvC,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,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,OAAO;gBACL,QAAQ;gBACR,KAAK,EAAE,cAAc;aACtB,CAAA;QACH,CAAC;QAED,OAAO;YACL,UAAU;YACV,aAAa;YACb,OAAO,EAAE,CAAC,KAAa,EAAE,EAAE;gBACzB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;oBAC7B,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBAChC,IAAI,MAAM,EAAE,CAAC;wBACX,YAAY,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;oBACjC,CAAC;oBACD,OAAO,MAAM,CAAA;gBACf,CAAC;gBACD,OAAO,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAChC,CAAC;YACD,QAAQ;YACR,GAAG,EAAE,IAAI;YACT,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,GAAG,GAAG;SACP,CAAA;IACH,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;QAEnB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAEnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAE/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,MAAM,GAAG,EAAE,CAAA;QACjB,sEAAsE;QACtE,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;YAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;gBACxC,MAAM,SAAS,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;gBAC/B,IAAI,SAAS,EAAE,CAAC;oBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;wBACjD,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAE,CAAC,CAAA;oBAC5B,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,IAAA,wBAAc,EAAC,MAAM,EAAE,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IACxD,CAAC;IAED;;;OAGG;IACH,QAAQ,CAAC,GAAW,EAAE,GAAW;QAC/B,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;QACvC,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC;YAClB,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;QACf,CAAC,CAAC,wCAAwC;QAC1C,GAAG,IAAI,CAAC,CAAA;QACR,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACtC,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,OAAO,CAAC,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9D,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;gBAC5C,MAAM,IAAI,KAAK,CACb,SAAS,GAAG,IAAI,GAAG,mDAAmD,IAAI,CAAC,QAAQ,WAAW,IAAI,CAAC,KAAK,0DAA0D,CACnK,CAAA;YACH,CAAC;YACD,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAU,CAAC,CAAA;QAC5B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAiB,EAAE;QAC7B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACnD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;QAChD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACrC,OAAO,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IAC1C,CAAC;CACF;AA3PD,sBA2PC"}
|
package/dist/record.js
CHANGED
|
@@ -9,8 +9,9 @@ const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
|
|
|
9
9
|
const ASCII_CIGAR_CODES = [
|
|
10
10
|
77, 73, 68, 78, 83, 72, 80, 61, 88, 63, 63, 63, 63, 63, 63, 63,
|
|
11
11
|
];
|
|
12
|
-
// ops that
|
|
13
|
-
|
|
12
|
+
// Bitmask for ops that consume ref: M=0, D=2, N=3, P=6, ==7, X=8
|
|
13
|
+
// Binary: 0b111001101 = 0x1CD
|
|
14
|
+
const CIGAR_CONSUMES_REF_MASK = 0x1cd;
|
|
14
15
|
class BamRecord {
|
|
15
16
|
constructor(args) {
|
|
16
17
|
this.bytes = args.bytes;
|
|
@@ -532,10 +533,7 @@ class BamRecord {
|
|
|
532
533
|
let lref = 0;
|
|
533
534
|
for (let c = 0; c < numCigarOps; ++c) {
|
|
534
535
|
const cigop = cigarView[c];
|
|
535
|
-
|
|
536
|
-
if (!((1 << op) & CIGAR_SKIP_MASK)) {
|
|
537
|
-
lref += cigop >> 4;
|
|
538
|
-
}
|
|
536
|
+
lref += (cigop >> 4) * ((CIGAR_CONSUMES_REF_MASK >> (cigop & 0xf)) & 1);
|
|
539
537
|
}
|
|
540
538
|
return {
|
|
541
539
|
NUMERIC_CIGAR: cigarView,
|
|
@@ -547,10 +545,7 @@ class BamRecord {
|
|
|
547
545
|
for (let c = 0; c < numCigarOps; ++c) {
|
|
548
546
|
const cigop = this._dataView.getInt32(p + c * 4, true) | 0;
|
|
549
547
|
cigarArray[c] = cigop;
|
|
550
|
-
|
|
551
|
-
if (!((1 << op) & CIGAR_SKIP_MASK)) {
|
|
552
|
-
lref = (lref + (cigop >> 4)) | 0;
|
|
553
|
-
}
|
|
548
|
+
lref += (cigop >> 4) * ((CIGAR_CONSUMES_REF_MASK >> (cigop & 0xf)) & 1);
|
|
554
549
|
}
|
|
555
550
|
return {
|
|
556
551
|
NUMERIC_CIGAR: cigarArray,
|
package/dist/record.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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package/esm/bai.js
CHANGED
package/esm/bai.js.map
CHANGED
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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,OAAO,QAAQ,MAAM,
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1
|
+
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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
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,QAAQ,MAAM,oBAAoB,CAAA;AAEzC,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EACL,aAAa,EACb,cAAc,EACd,cAAc,EACd,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAA1C;;QACU,iBAAY,GAAG,CAAC,CAAA;QAChB,UAAK,GAAG,CAAC,CAAA;QACT,aAAQ,GAAG,CAAC,CAAA;IAwPtB,CAAC;IApPC,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,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACpD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GACV,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EACnC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACpB,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,OAAO;YACL,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW;YACX,GAAG,cAAc,CACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAA8B;QACzC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACnD,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,IAAI,UAAU,CAAA;QACd,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAEzC,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;YAC1C,oDAAoD;QACtD,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACtE,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,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;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,IAAI,IAAI,CAAC,CAAA;oBACT,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,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;wBACT,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;oBACjD,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,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,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,cAAc,CAAA;YAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,cAAc,GAAG,cAAc,CAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC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|
package/esm/record.js
CHANGED
|
@@ -1,11 +1,12 @@
|
|
|
1
|
-
import {
|
|
1
|
+
import { CIGAR_REF_SKIP, CIGAR_SOFT_CLIP } from "./cigar.js";
|
|
2
2
|
import Constants from "./constants.js";
|
|
3
3
|
const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
|
|
4
4
|
const ASCII_CIGAR_CODES = [
|
|
5
5
|
77, 73, 68, 78, 83, 72, 80, 61, 88, 63, 63, 63, 63, 63, 63, 63,
|
|
6
6
|
];
|
|
7
|
-
// ops that
|
|
8
|
-
|
|
7
|
+
// Bitmask for ops that consume ref: M=0, D=2, N=3, P=6, ==7, X=8
|
|
8
|
+
// Binary: 0b111001101 = 0x1CD
|
|
9
|
+
const CIGAR_CONSUMES_REF_MASK = 0x1cd;
|
|
9
10
|
export default class BamRecord {
|
|
10
11
|
constructor(args) {
|
|
11
12
|
this.bytes = args.bytes;
|
|
@@ -527,10 +528,7 @@ export default class BamRecord {
|
|
|
527
528
|
let lref = 0;
|
|
528
529
|
for (let c = 0; c < numCigarOps; ++c) {
|
|
529
530
|
const cigop = cigarView[c];
|
|
530
|
-
|
|
531
|
-
if (!((1 << op) & CIGAR_SKIP_MASK)) {
|
|
532
|
-
lref += cigop >> 4;
|
|
533
|
-
}
|
|
531
|
+
lref += (cigop >> 4) * ((CIGAR_CONSUMES_REF_MASK >> (cigop & 0xf)) & 1);
|
|
534
532
|
}
|
|
535
533
|
return {
|
|
536
534
|
NUMERIC_CIGAR: cigarView,
|
|
@@ -542,10 +540,7 @@ export default class BamRecord {
|
|
|
542
540
|
for (let c = 0; c < numCigarOps; ++c) {
|
|
543
541
|
const cigop = this._dataView.getInt32(p + c * 4, true) | 0;
|
|
544
542
|
cigarArray[c] = cigop;
|
|
545
|
-
|
|
546
|
-
if (!((1 << op) & CIGAR_SKIP_MASK)) {
|
|
547
|
-
lref = (lref + (cigop >> 4)) | 0;
|
|
548
|
-
}
|
|
543
|
+
lref += (cigop >> 4) * ((CIGAR_CONSUMES_REF_MASK >> (cigop & 0xf)) & 1);
|
|
549
544
|
}
|
|
550
545
|
return {
|
|
551
546
|
NUMERIC_CIGAR: cigarArray,
|
package/esm/record.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
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1
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+
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;QACT,MAAM,SAAS,GAAG,GAAG,IAAI,CAAC,CAAA;QAE1B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,EAAE,CAAC,EAAE,CAAC;YACnC,MAAM,EAAE,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;YACtB,GAAG,CAAC,CAAC,EAAE,CAAC,GAAG,cAAc,CAAC,CAAC,EAAE,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAA;YAC3C,GAAG,CAAC,CAAC,EAAE,CAAC,GAAG,cAAc,CAAC,EAAE,GAAG,IAAI,CAAC,CAAA;QACtC,CAAC;QAED,IAAI,CAAC,GAAG,GAAG,EAAE,CAAC;YACZ,MAAM,EAAE,GAAG,OAAO,CAAC,SAAS,CAAE,CAAA;YAC9B,GAAG,CAAC,CAAC,CAAC,GAAG,cAAc,CAAC,CAAC,EAAE,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAA;QAC3C,CAAC;QAED,OAAO,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IACrB,CAAC;IAED,sBAAsB;IACtB,qGAAqG;IACrG,IAAI,gBAAgB;QAClB,IACE,CAAC,IAAI,CAAC,iBAAiB,EAAE;YACzB,CAAC,IAAI,CAAC,cAAc,EAAE;YACtB,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,UAAU,EAC/B,CAAC;YACD,MAAM,EAAE,GAAG,IAAI,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAA;YACnD,MAAM,EAAE,GAAG,IAAI,CAAC,yBAAyB,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAA;YACvD,IAAI,EAAE,GAAG,GAAG,CAAA;YACZ,IAAI,EAAE,GAAG,GAAG,CAAA;YACZ,IAAI,IAAI,CAAC,OAAO,EAAE,EAAE,CAAC;gBACnB,EAAE,GAAG,GAAG,CAAA;gBACR,EAAE,GAAG,GAAG,CAAA;YACV,CAAC;iBAAM,IAAI,IAAI,CAAC,OAAO,EAAE,EAAE,CAAC;gBAC1B,EAAE,GAAG,GAAG,CAAA;gBACR,EAAE,GAAG,GAAG,CAAA;YACV,CAAC;YAED,OAAO,IAAI,CAAC,eAAe,GAAG,CAAC;gBAC7B,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE;gBACxB,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,CAAA;QAC5B,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,SAAS;QACX,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC7D,CAAC;IAED,IAAI,OAAO;QACT,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC7D,CAAC;IAED,IAAI,UAAU;QACZ,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC7D,CAAC;IAED,IAAI,UAAU;QACZ,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC7D,CAAC;IAED,IAAI,QAAQ;QACV,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC7D,CAAC;IAED,IAAI,eAAe;QACjB,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC7D,CAAC;IAED,KAAK,CAAC,GAAW;QACf,IAAI,GAAG,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC;YAC1B,MAAM,SAAS,GAAG,GAAG,IAAI,CAAC,CAAA;YAC1B,MAAM,EAAE,GACN,IAAI,CAAC,SAAS,CACZ,IAAI,CAAC,EAAE,GAAG,IAAI,CAAC,gBAAgB,GAAG,IAAI,CAAC,eAAe,GAAG,SAAS,CAClE,CAAA;YAEJ,OAAO,GAAG,GAAG,CAAC,KAAK,CAAC;gBAClB,CAAC,CAAC,cAAc,CAAC,CAAC,EAAE,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC;gBAClC,CAAC,CAAC,cAAc,CAAC,EAAE,GAAG,IAAI,CAAC,CAAA;QAC/B,CAAC;aAAM,CAAC;YACN,OAAO,SAAS,CAAA;QAClB,CAAC;IACH,CAAC;IAED,MAAM;QACJ,MAAM,IAAI,GAAwB,EAAE,CAAA;QACpC,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAClC,IAAI,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,OAAO,EAAE,CAAC;gBACvC,SAAQ;YACV,CAAC;YACD,aAAa;YACb,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACnB,CAAC;QAED,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/bam",
|
|
3
|
-
"version": "7.1.
|
|
3
|
+
"version": "7.1.14",
|
|
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": "^6.0.8",
|
|
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/csi.ts
CHANGED
package/src/record.ts
CHANGED
|
@@ -1,9 +1,4 @@
|
|
|
1
|
-
import {
|
|
2
|
-
CIGAR_HARD_CLIP,
|
|
3
|
-
CIGAR_INS,
|
|
4
|
-
CIGAR_REF_SKIP,
|
|
5
|
-
CIGAR_SOFT_CLIP,
|
|
6
|
-
} from './cigar.ts'
|
|
1
|
+
import { CIGAR_REF_SKIP, CIGAR_SOFT_CLIP } from './cigar.ts'
|
|
7
2
|
import Constants from './constants.ts'
|
|
8
3
|
|
|
9
4
|
const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('')
|
|
@@ -11,9 +6,9 @@ const ASCII_CIGAR_CODES = [
|
|
|
11
6
|
77, 73, 68, 78, 83, 72, 80, 61, 88, 63, 63, 63, 63, 63, 63, 63,
|
|
12
7
|
]
|
|
13
8
|
|
|
14
|
-
// ops that
|
|
15
|
-
|
|
16
|
-
|
|
9
|
+
// Bitmask for ops that consume ref: M=0, D=2, N=3, P=6, ==7, X=8
|
|
10
|
+
// Binary: 0b111001101 = 0x1CD
|
|
11
|
+
const CIGAR_CONSUMES_REF_MASK = 0x1cd
|
|
17
12
|
|
|
18
13
|
export interface Bytes {
|
|
19
14
|
start: number
|
|
@@ -584,10 +579,7 @@ export default class BamRecord {
|
|
|
584
579
|
let lref = 0
|
|
585
580
|
for (let c = 0; c < numCigarOps; ++c) {
|
|
586
581
|
const cigop = cigarView[c]!
|
|
587
|
-
|
|
588
|
-
if (!((1 << op) & CIGAR_SKIP_MASK)) {
|
|
589
|
-
lref += cigop >> 4
|
|
590
|
-
}
|
|
582
|
+
lref += (cigop >> 4) * ((CIGAR_CONSUMES_REF_MASK >> (cigop & 0xf)) & 1)
|
|
591
583
|
}
|
|
592
584
|
return {
|
|
593
585
|
NUMERIC_CIGAR: cigarView,
|
|
@@ -600,10 +592,7 @@ export default class BamRecord {
|
|
|
600
592
|
for (let c = 0; c < numCigarOps; ++c) {
|
|
601
593
|
const cigop = this._dataView.getInt32(p + c * 4, true) | 0
|
|
602
594
|
cigarArray[c] = cigop
|
|
603
|
-
|
|
604
|
-
if (!((1 << op) & CIGAR_SKIP_MASK)) {
|
|
605
|
-
lref = (lref + (cigop >> 4)) | 0
|
|
606
|
-
}
|
|
595
|
+
lref += (cigop >> 4) * ((CIGAR_CONSUMES_REF_MASK >> (cigop & 0xf)) & 1)
|
|
607
596
|
}
|
|
608
597
|
return {
|
|
609
598
|
NUMERIC_CIGAR: cigarArray,
|