@gmod/bam 7.3.2 → 7.3.4
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/dist/bai.js +1 -0
- package/dist/bai.js.map +1 -1
- package/dist/chunk.d.ts +2 -2
- package/dist/chunk.js +8 -7
- package/dist/chunk.js.map +1 -1
- package/dist/csi.js +1 -0
- package/dist/csi.js.map +1 -1
- package/dist/long.d.ts +0 -2
- package/dist/long.js +2 -4
- package/dist/long.js.map +1 -1
- package/dist/record.d.ts +1 -1
- package/dist/record.js +93 -143
- package/dist/record.js.map +1 -1
- package/dist/util.d.ts +1 -0
- package/dist/util.js +34 -1
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.d.ts +1 -1
- package/dist/virtualOffset.js +1 -4
- package/dist/virtualOffset.js.map +1 -1
- package/esm/bai.js +2 -1
- package/esm/bai.js.map +1 -1
- package/esm/chunk.d.ts +2 -2
- package/esm/chunk.js +8 -7
- package/esm/chunk.js.map +1 -1
- package/esm/csi.js +2 -1
- package/esm/csi.js.map +1 -1
- package/esm/long.d.ts +0 -2
- package/esm/long.js +1 -2
- package/esm/long.js.map +1 -1
- package/esm/record.d.ts +1 -1
- package/esm/record.js +93 -143
- package/esm/record.js.map +1 -1
- package/esm/util.d.ts +1 -0
- package/esm/util.js +33 -1
- package/esm/util.js.map +1 -1
- package/esm/virtualOffset.d.ts +1 -1
- package/esm/virtualOffset.js +1 -4
- package/esm/virtualOffset.js.map +1 -1
- package/package.json +1 -1
- package/src/bai.ts +5 -1
- package/src/chunk.ts +20 -9
- package/src/csi.ts +7 -1
- package/src/long.ts +1 -2
- package/src/record.ts +116 -150
- package/src/util.ts +34 -0
- package/src/virtualOffset.ts +1 -5
package/dist/bai.js
CHANGED
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@@ -153,6 +153,7 @@ class BAI extends indexFile_ts_1.default {
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linearIndex[j] = (0, virtualOffset_ts_1.fromBytes)(bytes, curr);
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curr += 8;
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}
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+
(0, util_ts_1.clampChunkEnds)(Object.values(binIndex).flat(), linearIndex.map(v => v.blockPosition));
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return {
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binIndex,
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linearIndex,
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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,0DAA8B;AAC9B,+DAA0D;AAC1D,
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1
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+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,0DAA8B;AAC9B,+DAA0D;AAC1D,uCAAyE;AACzE,yDAA8C;AAc9C,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,4EAA4E;AAC5E,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAC3B,MAAM,mBAAmB,GAAG,CAAC,IAAI,gBAAgB,CAAA,CAAC,QAAQ;AAE1D,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,4EAA4E;AAC5E,qEAAqE;AACrE,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,gBAAgB,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,gBAAgB,CAAC,CAAC;KAC5D,CAAA;AACZ,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAoB;IACnD,KAAK,CAAC,MAAM,CAAC,IAAc;QACzB,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAClD,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,mEAAmE;YACnE,kDAAkD;YAClD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;gBACpE,IAAI,IAAI,CAAC,CAAA;YACX,CAAC;QACH,CAAC;QAED,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,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,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,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACvC,IAAI,IAAI,CAAC,CAAA;YACX,CAAC;YAED,IAAA,wBAAc,EACZ,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,EAC9B,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CACtC,CAAA;YACD,OAAO;gBACL,QAAQ;gBACR,WAAW;gBACX,KAAK;aACN,CAAA;QACH,CAAC;QAED,OAAO;YACL,GAAG,EAAE,IAAI;YACT,aAAa;YACb,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,OAAO,EAAE,IAAA,6BAAc,EAAC,UAAU,CAAC;YACnC,QAAQ;SACT,CAAA;IACH,CAAC;IAED,KAAK,CAAC,QAAQ,CACZ,KAAa,EACb,KAAc,EACd,GAAY,EACZ,IAAe;QAEf,MAAM,CAAC,GAAG,mBAAmB,CAAA;QAC7B,MAAM,KAAK,GAAG,KAAK,KAAK,SAAS,CAAA;QACjC,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAEvC,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;QACrC,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;QAC5E,MAAM,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;QACvD,MAAM,MAAM,GAAG,KAAK;YAClB,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;YACxB,CAAC,CAAC,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,MAAM,SAAS,GAAG,WAAW,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAE,CAAC,aAAa,CAAA;QACpE,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;QAC3D,CAAC;QACD,IAAI,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,aAAa,CAAA;QAClD,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YAC/C,MAAM,CAAC,CAAC,CAAC,GAAG;gBACV,KAAK,EAAE,WAAW,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,aAAa,GAAG,UAAU;gBACrD,KAAK,EAAE,CAAC,GAAG,CAAC;gBACZ,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC;aACf,CAAA;YACD,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,aAAa,CAAA;QAChD,CAAC;QACD,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YACtB,GAAG,CAAC;YACJ,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,EAAE,SAAS,IAAI,CAAC,CAAC,CAAC,GAAG,SAAS;SACvD,CAAC,CAAC,CAAA;IACL,CAAC;IAES,QAAQ,CAAC,GAAW,EAAE,GAAW;QACzC,OAAO,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;IAC3B,CAAC;IAED,0EAA0E;IAC1E,2EAA2E;IAC3E,+DAA+D;IACrD,cAAc,CAAC,QAAqB,EAAE,GAAW;QACzD,MAAM,EAAE,WAAW,EAAE,GAAG,QAAQ,CAAA;QAChC,MAAM,KAAK,GAAG,WAAW,CAAC,MAAM,CAAA;QAChC,OAAO,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,gBAAgB,EAAE,KAAK,GAAG,CAAC,CAAC,CAAC,CAAA;IAClE,CAAC;CACF;AA1KD,sBA0KC"}
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package/dist/chunk.d.ts
CHANGED
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@@ -3,8 +3,8 @@ export default class Chunk {
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constructor(minv: Offset, maxv: Offset, bin: number,
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constructor(minv: Offset, maxv: Offset, bin: number, endPosition?: number);
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CHANGED
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this.bin - b.bin);
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package/dist/chunk.js.map
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{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;
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{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IACjB,IAAI,CAAQ;IACZ,IAAI,CAAQ;IACZ,GAAG,CAAQ;IAClB,2EAA2E;IAC3E,0EAA0E;IAC1E,8EAA8E;IAC9E,oEAAoE;IAC7D,WAAW,CAAQ;IAE1B,YACE,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,WAAW,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;QAE5C,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACnD,CAAC;CACF;AAvCD,wBAuCC"}
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package/dist/csi.js
CHANGED
package/dist/csi.js.map
CHANGED
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{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,+DAA0D;AAC1D,
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|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,+DAA0D;AAC1D,uCAKkB;AAClB,yDAA6D;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,WAAW,GAAG,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAE3C,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;IAChC,YAAY,GAAG,CAAC,CAAA;IAChB,KAAK,GAAG,CAAC,CAAA;IACT,QAAQ,GAAG,CAAC,CAAA;IAEpB,uEAAuE;IACvE,iEAAiE;IACjE,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,GAAG,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QAC3D,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,IAAc;QACzB,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,mEAAmE;QACnE,+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,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,IAAI,IAAI,CAAC,CAAA,CAAC,6DAA6D;oBACvE,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,IAAA,wBAAc,EAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;YAC9C,OAAO;gBACL,QAAQ;gBACR,KAAK,EAAE,cAAc;aACtB,CAAA;QACH,CAAC;QAED,OAAO;YACL,UAAU;YACV,aAAa;YACb,OAAO,EAAE,IAAA,6BAAc,EAAC,UAAU,CAAC;YACnC,QAAQ;YACR,GAAG,EAAE,IAAI;YACT,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,GAAG,GAAG;SACP,CAAA;IACH,CAAC;IAED,2EAA2E;IACjE,cAAc;QACtB,OAAO,WAAW,CAAA;IACpB,CAAC;IAED;;;;OAIG;IACH,gDAAgD;IACtC,QAAQ,CAAC,GAAW,EAAE,GAAW;QACzC,2EAA2E;QAC3E,wEAAwE;QACxE,MAAM,MAAM,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QACpD,IAAI,GAAG,GAAG,MAAM,EAAE,CAAC;YACjB,GAAG,GAAG,MAAM,CAAA;QACd,CAAC;QACD,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;CACF;AAxLD,sBAwLC"}
|
package/dist/long.d.ts
CHANGED
package/dist/long.js
CHANGED
|
@@ -1,9 +1,7 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.TWO_PWR_32_DBL = exports.TWO_PWR_16_DBL = void 0;
|
|
4
3
|
exports.longFromBytesToUnsigned = longFromBytesToUnsigned;
|
|
5
|
-
|
|
6
|
-
exports.TWO_PWR_32_DBL = exports.TWO_PWR_16_DBL * exports.TWO_PWR_16_DBL;
|
|
4
|
+
const TWO_PWR_32_DBL = 2 ** 32;
|
|
7
5
|
// avoids dependency on long.js
|
|
8
6
|
function longFromBytesToUnsigned(source, i = 0) {
|
|
9
7
|
const low = source[i] |
|
|
@@ -14,6 +12,6 @@ function longFromBytesToUnsigned(source, i = 0) {
|
|
|
14
12
|
(source[i + 5] << 8) |
|
|
15
13
|
(source[i + 6] << 16) |
|
|
16
14
|
(source[i + 7] << 24);
|
|
17
|
-
return (high >>> 0) *
|
|
15
|
+
return (high >>> 0) * TWO_PWR_32_DBL + (low >>> 0);
|
|
18
16
|
}
|
|
19
17
|
//# sourceMappingURL=long.js.map
|
package/dist/long.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":";;AAGA,0DAYC;AAfD,MAAM,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AAE9B,+BAA+B;AAC/B,SAAgB,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,cAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}
|
package/dist/record.d.ts
CHANGED
|
@@ -36,7 +36,7 @@ export default class BamRecord {
|
|
|
36
36
|
get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
|
|
37
37
|
get tags(): Record<string, unknown>;
|
|
38
38
|
getTag(tagName: string): unknown;
|
|
39
|
-
getTagRaw(tagName: string):
|
|
39
|
+
getTagRaw(tagName: string): unknown;
|
|
40
40
|
private _findTag;
|
|
41
41
|
private _computeTags;
|
|
42
42
|
isPaired(): boolean;
|
package/dist/record.js
CHANGED
|
@@ -105,6 +105,82 @@ function bArrayByteLength(Btype, limit) {
|
|
|
105
105
|
return limit;
|
|
106
106
|
}
|
|
107
107
|
}
|
|
108
|
+
// Cursor position just past a tag's value — i.e. the start of the next tag —
|
|
109
|
+
// given the value starts at `p`. For null-terminated Z/H this steps over the
|
|
110
|
+
// terminator. Returns 0 for an unknown type, whose value width is unknowable so
|
|
111
|
+
// the caller must stop. Shared by _findTag and _computeTags so the two loops
|
|
112
|
+
// can't drift in how they walk the tag layout. (0 is an impossible real end:
|
|
113
|
+
// `p` is always past the fixed record prefix.)
|
|
114
|
+
function tagValueEnd(ba, dataView, type, p, blockEnd) {
|
|
115
|
+
switch (type) {
|
|
116
|
+
case 0x41: // 'A'
|
|
117
|
+
case 0x63: // 'c'
|
|
118
|
+
case 0x43: // 'C'
|
|
119
|
+
return p + 1;
|
|
120
|
+
case 0x73: // 's'
|
|
121
|
+
case 0x53: // 'S'
|
|
122
|
+
return p + 2;
|
|
123
|
+
case 0x69: // 'i'
|
|
124
|
+
case 0x49: // 'I'
|
|
125
|
+
case 0x66: {
|
|
126
|
+
// 'f'
|
|
127
|
+
return p + 4;
|
|
128
|
+
}
|
|
129
|
+
case 0x5a: // 'Z'
|
|
130
|
+
case 0x48: {
|
|
131
|
+
// 'H'
|
|
132
|
+
let q = p;
|
|
133
|
+
while (q < blockEnd && ba[q] !== 0) {
|
|
134
|
+
q++;
|
|
135
|
+
}
|
|
136
|
+
return q + 1; // step past the null terminator
|
|
137
|
+
}
|
|
138
|
+
case 0x42: {
|
|
139
|
+
// 'B'
|
|
140
|
+
const Btype = ba[p];
|
|
141
|
+
const limit = dataView.getInt32(p + 1, true);
|
|
142
|
+
return p + 5 + bArrayByteLength(Btype, limit);
|
|
143
|
+
}
|
|
144
|
+
default:
|
|
145
|
+
console.error('Unknown BAM tag type', type);
|
|
146
|
+
return 0;
|
|
147
|
+
}
|
|
148
|
+
}
|
|
149
|
+
// Decode the value of a tag of `type` whose bytes start at `p`; `end` is the
|
|
150
|
+
// next-tag cursor from tagValueEnd (used only to bound Z/H strings, whose bytes
|
|
151
|
+
// run up to the null terminator at end-1). When `raw`, Z/H return the undecoded
|
|
152
|
+
// byte subarray. Assumes `type` is a known scalar/string/B type.
|
|
153
|
+
function decodeTagValue(ba, dataView, type, p, end, raw) {
|
|
154
|
+
switch (type) {
|
|
155
|
+
case 0x41: // 'A'
|
|
156
|
+
return String.fromCharCode(ba[p]);
|
|
157
|
+
case 0x69: // 'i'
|
|
158
|
+
return dataView.getInt32(p, true);
|
|
159
|
+
case 0x49: // 'I'
|
|
160
|
+
return dataView.getUint32(p, true);
|
|
161
|
+
case 0x63: // 'c'
|
|
162
|
+
return dataView.getInt8(p);
|
|
163
|
+
case 0x43: // 'C'
|
|
164
|
+
return dataView.getUint8(p);
|
|
165
|
+
case 0x73: // 's'
|
|
166
|
+
return dataView.getInt16(p, true);
|
|
167
|
+
case 0x53: // 'S'
|
|
168
|
+
return dataView.getUint16(p, true);
|
|
169
|
+
case 0x66: // 'f'
|
|
170
|
+
return dataView.getFloat32(p, true);
|
|
171
|
+
case 0x5a: // 'Z'
|
|
172
|
+
case 0x48: // 'H'
|
|
173
|
+
return raw
|
|
174
|
+
? ba.subarray(p, end - 1)
|
|
175
|
+
: textDecoder.decode(ba.subarray(p, end - 1));
|
|
176
|
+
default: {
|
|
177
|
+
// 'B'
|
|
178
|
+
const Btype = ba[p];
|
|
179
|
+
const limit = dataView.getInt32(p + 1, true);
|
|
180
|
+
return decodeBArrayTag(ba, dataView, p + 5, Btype, limit);
|
|
181
|
+
}
|
|
182
|
+
}
|
|
183
|
+
}
|
|
108
184
|
class BamRecord {
|
|
109
185
|
fileOffset;
|
|
110
186
|
_byteArray;
|
|
@@ -220,165 +296,39 @@ class BamRecord {
|
|
|
220
296
|
_findTag(tagName, raw) {
|
|
221
297
|
const tag1 = tagName.charCodeAt(0);
|
|
222
298
|
const tag2 = tagName.charCodeAt(1);
|
|
223
|
-
let p = this.tagsStart;
|
|
224
299
|
const blockEnd = this._end;
|
|
225
300
|
const ba = this._byteArray;
|
|
301
|
+
let p = this.tagsStart;
|
|
226
302
|
while (p < blockEnd) {
|
|
227
|
-
const
|
|
228
|
-
const currentTag2 = ba[p + 1];
|
|
303
|
+
const isMatch = ba[p] === tag1 && ba[p + 1] === tag2;
|
|
229
304
|
const type = ba[p + 2];
|
|
230
|
-
p
|
|
231
|
-
const
|
|
232
|
-
|
|
233
|
-
|
|
234
|
-
|
|
235
|
-
|
|
236
|
-
|
|
237
|
-
p += 1;
|
|
238
|
-
break;
|
|
239
|
-
case 0x69: // 'i'
|
|
240
|
-
if (isMatch) {
|
|
241
|
-
return this._dataView.getInt32(p, true);
|
|
242
|
-
}
|
|
243
|
-
p += 4;
|
|
244
|
-
break;
|
|
245
|
-
case 0x49: // 'I'
|
|
246
|
-
if (isMatch) {
|
|
247
|
-
return this._dataView.getUint32(p, true);
|
|
248
|
-
}
|
|
249
|
-
p += 4;
|
|
250
|
-
break;
|
|
251
|
-
case 0x63: // 'c'
|
|
252
|
-
if (isMatch) {
|
|
253
|
-
return this._dataView.getInt8(p);
|
|
254
|
-
}
|
|
255
|
-
p += 1;
|
|
256
|
-
break;
|
|
257
|
-
case 0x43: // 'C'
|
|
258
|
-
if (isMatch) {
|
|
259
|
-
return this._dataView.getUint8(p);
|
|
260
|
-
}
|
|
261
|
-
p += 1;
|
|
262
|
-
break;
|
|
263
|
-
case 0x73: // 's'
|
|
264
|
-
if (isMatch) {
|
|
265
|
-
return this._dataView.getInt16(p, true);
|
|
266
|
-
}
|
|
267
|
-
p += 2;
|
|
268
|
-
break;
|
|
269
|
-
case 0x53: // 'S'
|
|
270
|
-
if (isMatch) {
|
|
271
|
-
return this._dataView.getUint16(p, true);
|
|
272
|
-
}
|
|
273
|
-
p += 2;
|
|
274
|
-
break;
|
|
275
|
-
case 0x66: // 'f'
|
|
276
|
-
if (isMatch) {
|
|
277
|
-
return this._dataView.getFloat32(p, true);
|
|
278
|
-
}
|
|
279
|
-
p += 4;
|
|
280
|
-
break;
|
|
281
|
-
case 0x5a: // 'Z'
|
|
282
|
-
case 0x48: {
|
|
283
|
-
// 'H'
|
|
284
|
-
const start = p;
|
|
285
|
-
while (p < blockEnd && ba[p] !== 0) {
|
|
286
|
-
p++;
|
|
287
|
-
}
|
|
288
|
-
if (isMatch) {
|
|
289
|
-
return raw
|
|
290
|
-
? ba.subarray(start, p)
|
|
291
|
-
: textDecoder.decode(ba.subarray(start, p));
|
|
292
|
-
}
|
|
293
|
-
p++; // advance past null terminator
|
|
294
|
-
break;
|
|
295
|
-
}
|
|
296
|
-
case 0x42: {
|
|
297
|
-
// 'B'
|
|
298
|
-
const Btype = ba[p++];
|
|
299
|
-
const limit = this._dataView.getInt32(p, true);
|
|
300
|
-
p += 4;
|
|
301
|
-
if (isMatch) {
|
|
302
|
-
return decodeBArrayTag(ba, this._dataView, p, Btype, limit);
|
|
303
|
-
}
|
|
304
|
-
p += bArrayByteLength(Btype, limit);
|
|
305
|
-
break;
|
|
306
|
-
}
|
|
307
|
-
default:
|
|
308
|
-
if (type !== undefined) {
|
|
309
|
-
console.error('Unknown BAM tag type', type);
|
|
310
|
-
}
|
|
311
|
-
break;
|
|
305
|
+
const valueStart = p + 3;
|
|
306
|
+
const end = tagValueEnd(ba, this._dataView, type, valueStart, blockEnd);
|
|
307
|
+
if (end === 0) {
|
|
308
|
+
break; // unknown type: can't compute how far to advance
|
|
309
|
+
}
|
|
310
|
+
if (isMatch) {
|
|
311
|
+
return decodeTagValue(ba, this._dataView, type, valueStart, end, raw);
|
|
312
312
|
}
|
|
313
|
+
p = end;
|
|
313
314
|
}
|
|
314
315
|
return undefined;
|
|
315
316
|
}
|
|
316
317
|
_computeTags() {
|
|
317
|
-
let p = this.tagsStart;
|
|
318
318
|
const blockEnd = this._end;
|
|
319
319
|
const ba = this._byteArray;
|
|
320
320
|
const tags = {};
|
|
321
|
+
let p = this.tagsStart;
|
|
321
322
|
while (p < blockEnd) {
|
|
322
323
|
const tag = String.fromCharCode(ba[p], ba[p + 1]);
|
|
323
324
|
const type = ba[p + 2];
|
|
324
|
-
p
|
|
325
|
-
|
|
326
|
-
|
|
327
|
-
|
|
328
|
-
p += 1;
|
|
329
|
-
break;
|
|
330
|
-
case 0x69: // 'i'
|
|
331
|
-
tags[tag] = this._dataView.getInt32(p, true);
|
|
332
|
-
p += 4;
|
|
333
|
-
break;
|
|
334
|
-
case 0x49: // 'I'
|
|
335
|
-
tags[tag] = this._dataView.getUint32(p, true);
|
|
336
|
-
p += 4;
|
|
337
|
-
break;
|
|
338
|
-
case 0x63: // 'c'
|
|
339
|
-
tags[tag] = this._dataView.getInt8(p);
|
|
340
|
-
p += 1;
|
|
341
|
-
break;
|
|
342
|
-
case 0x43: // 'C'
|
|
343
|
-
tags[tag] = this._dataView.getUint8(p);
|
|
344
|
-
p += 1;
|
|
345
|
-
break;
|
|
346
|
-
case 0x73: // 's'
|
|
347
|
-
tags[tag] = this._dataView.getInt16(p, true);
|
|
348
|
-
p += 2;
|
|
349
|
-
break;
|
|
350
|
-
case 0x53: // 'S'
|
|
351
|
-
tags[tag] = this._dataView.getUint16(p, true);
|
|
352
|
-
p += 2;
|
|
353
|
-
break;
|
|
354
|
-
case 0x66: // 'f'
|
|
355
|
-
tags[tag] = this._dataView.getFloat32(p, true);
|
|
356
|
-
p += 4;
|
|
357
|
-
break;
|
|
358
|
-
case 0x5a: // 'Z'
|
|
359
|
-
case 0x48: {
|
|
360
|
-
// 'H'
|
|
361
|
-
const start = p;
|
|
362
|
-
while (p < blockEnd && ba[p] !== 0) {
|
|
363
|
-
p++;
|
|
364
|
-
}
|
|
365
|
-
tags[tag] = textDecoder.decode(ba.subarray(start, p));
|
|
366
|
-
p++; // advance past null terminator
|
|
367
|
-
break;
|
|
368
|
-
}
|
|
369
|
-
case 0x42: {
|
|
370
|
-
// 'B'
|
|
371
|
-
const Btype = ba[p++];
|
|
372
|
-
const limit = this._dataView.getInt32(p, true);
|
|
373
|
-
p += 4;
|
|
374
|
-
tags[tag] = decodeBArrayTag(ba, this._dataView, p, Btype, limit);
|
|
375
|
-
p += bArrayByteLength(Btype, limit);
|
|
376
|
-
break;
|
|
377
|
-
}
|
|
378
|
-
default:
|
|
379
|
-
console.error('Unknown BAM tag type', type);
|
|
380
|
-
break;
|
|
325
|
+
const valueStart = p + 3;
|
|
326
|
+
const end = tagValueEnd(ba, this._dataView, type, valueStart, blockEnd);
|
|
327
|
+
if (end === 0) {
|
|
328
|
+
break; // unknown type: can't compute how far to advance
|
|
381
329
|
}
|
|
330
|
+
tags[tag] = decodeTagValue(ba, this._dataView, type, valueStart, end, false);
|
|
331
|
+
p = end;
|
|
382
332
|
}
|
|
383
333
|
return tags;
|
|
384
334
|
}
|
package/dist/record.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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|
package/dist/util.d.ts
CHANGED
|
@@ -38,6 +38,7 @@ export declare function optimizeChunks(chunks: Chunk[], lowest?: Offset): Chunk[
|
|
|
38
38
|
export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
|
|
39
39
|
lineCount: number;
|
|
40
40
|
};
|
|
41
|
+
export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number[]): void;
|
|
41
42
|
export declare function parseRefSeqs(uncba: Uint8Array, start: number, renameRefSeq: (s: string) => string): {
|
|
42
43
|
chrToIndex: Record<string, number>;
|
|
43
44
|
indexToChr: {
|
package/dist/util.js
CHANGED
|
@@ -5,6 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
exports.optimizeChunks = optimizeChunks;
|
|
7
7
|
exports.parsePseudoBin = parsePseudoBin;
|
|
8
|
+
exports.clampChunkEnds = clampChunkEnds;
|
|
8
9
|
exports.parseRefSeqs = parseRefSeqs;
|
|
9
10
|
exports.findFirstData = findFirstData;
|
|
10
11
|
exports.parseNameBytes = parseNameBytes;
|
|
@@ -63,7 +64,7 @@ function optimizeChunks(chunks, lowest) {
|
|
|
63
64
|
const cmp = chunkMaxBlock - lastMaxBlock ||
|
|
64
65
|
chunk.maxv.dataPosition - lastChunk.maxv.dataPosition;
|
|
65
66
|
if (cmp > 0) {
|
|
66
|
-
mergedChunks[mergedChunks.length - 1] = new chunk_ts_1.default(lastChunk.minv, chunk.maxv, lastChunk.bin);
|
|
67
|
+
mergedChunks[mergedChunks.length - 1] = new chunk_ts_1.default(lastChunk.minv, chunk.maxv, lastChunk.bin, chunk.endPosition);
|
|
67
68
|
lastMaxBlock = chunkMaxBlock;
|
|
68
69
|
}
|
|
69
70
|
}
|
|
@@ -80,6 +81,38 @@ function parsePseudoBin(bytes, offset) {
|
|
|
80
81
|
lineCount: (0, long_ts_1.longFromBytesToUnsigned)(bytes, offset),
|
|
81
82
|
};
|
|
82
83
|
}
|
|
84
|
+
// Tighten each chunk's endPosition (default: a full max-size BGZF block past
|
|
85
|
+
// maxv) down to the next known block boundary. Every chunk min/maxv blockPosition
|
|
86
|
+
// and every extraBoundary (e.g. linear-index entries) is a real BGZF block start;
|
|
87
|
+
// since blocks don't overlap, the first boundary strictly greater than a chunk's
|
|
88
|
+
// maxv.blockPosition is an upper bound on where that final block ends — always at
|
|
89
|
+
// least the true block end, so the clamped fetch still contains the whole block.
|
|
90
|
+
// Shrinks both the byte estimate and the actual fetch with no extra I/O.
|
|
91
|
+
function clampChunkEnds(chunks, extraBoundaries = []) {
|
|
92
|
+
const boundaries = [...extraBoundaries];
|
|
93
|
+
for (const c of chunks) {
|
|
94
|
+
boundaries.push(c.minv.blockPosition, c.maxv.blockPosition);
|
|
95
|
+
}
|
|
96
|
+
boundaries.sort((a, b) => a - b);
|
|
97
|
+
for (const c of chunks) {
|
|
98
|
+
const max = c.maxv.blockPosition;
|
|
99
|
+
// first boundary strictly greater than max
|
|
100
|
+
let lo = 0;
|
|
101
|
+
let hi = boundaries.length;
|
|
102
|
+
while (lo < hi) {
|
|
103
|
+
const mid = (lo + hi) >>> 1;
|
|
104
|
+
if (boundaries[mid] > max) {
|
|
105
|
+
hi = mid;
|
|
106
|
+
}
|
|
107
|
+
else {
|
|
108
|
+
lo = mid + 1;
|
|
109
|
+
}
|
|
110
|
+
}
|
|
111
|
+
if (lo < boundaries.length) {
|
|
112
|
+
c.endPosition = Math.min(c.endPosition, boundaries[lo]);
|
|
113
|
+
}
|
|
114
|
+
}
|
|
115
|
+
}
|
|
83
116
|
// Parse the BAM reference-sequence table (SAMv1.pdf §4.2). Returns undefined
|
|
84
117
|
// if `uncba` doesn't yet contain the full table — caller fetches more bytes
|
|
85
118
|
// and retries.
|