@gmod/bam 1.1.12 → 1.1.15
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 +21 -11
- package/dist/bai.d.ts +1 -1
- package/dist/bai.js +37 -49
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +3 -2
- package/dist/bamFile.js +211 -226
- package/dist/bamFile.js.map +1 -1
- package/dist/csi.js +6 -7
- package/dist/csi.js.map +1 -1
- package/dist/htsget.js +5 -1
- package/dist/htsget.js.map +1 -1
- package/dist/record.d.ts +8 -8
- package/dist/record.js +26 -33
- package/dist/record.js.map +1 -1
- package/esm/bai.d.ts +1 -1
- package/esm/bai.js +2 -3
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +3 -2
- package/esm/bamFile.js +78 -89
- package/esm/bamFile.js.map +1 -1
- package/esm/csi.js +1 -6
- package/esm/csi.js.map +1 -1
- package/esm/record.d.ts +8 -8
- package/esm/record.js +26 -33
- package/esm/record.js.map +1 -1
- package/package.json +15 -17
package/dist/csi.js
CHANGED
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@@ -16,7 +16,11 @@ var __extends = (this && this.__extends) || (function () {
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})();
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var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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if (k2 === undefined) k2 = k;
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Object.
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var desc = Object.getOwnPropertyDescriptor(m, k);
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if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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desc = { enumerable: true, get: function() { return m[k]; } };
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}
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Object.defineProperty(o, k2, desc);
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}) : (function(o, m, k, k2) {
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if (k2 === undefined) k2 = k;
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o[k2] = m[k];
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@@ -148,7 +152,7 @@ var CSI = /** @class */ (function (_super) {
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data.metaChar = data.metaValue ? String.fromCharCode(data.metaValue) : '';
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data.skipLines = bytes.readInt32LE(offset + 20);
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var nameSectionLength = bytes.readInt32LE(offset + 24);
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-
Object.assign(data, this._parseNameBytes(bytes.
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Object.assign(data, this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength)));
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return data;
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};
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CSI.prototype._parseNameBytes = function (namesBytes) {
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@@ -257,11 +261,6 @@ var CSI = /** @class */ (function (_super) {
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});
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};
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CSI.prototype.parsePseudoBin = function (bytes, offset) {
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// const one = Long.fromBytesLE(bytes.slice(offset + 4, offset + 12), true)
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-
// const two = Long.fromBytesLE(bytes.slice(offset + 12, offset + 20), true)
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// const three = longToNumber(
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// Long.fromBytesLE(bytes.slice(offset + 20, offset + 28), true),
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// )
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var lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset + 28, offset + 36), true));
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return { lineCount: lineCount };
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};
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package/dist/csi.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"
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{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,8CAAuB;AACvB,yDAA6C;AAC7C,+DAA0D;AAC1D,kDAA2B;AAC3B,+BAAgF;AAEhF,0DAAmC;AAEnC,IAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,IAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAC,CAAA;AACpC,CAAC;AAED;IAAiC,uBAAS;IAIxC,aAAY,IAAS;QAArB,YACE,kBAAM,IAAI,CAAC,SAIZ;QAHC,KAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,KAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,KAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;;IACnB,CAAC;IACK,uBAAS,GAAf,UAAgB,KAAa;;;;;4BACT,qBAAM,IAAI,CAAC,KAAK,EAAE,EAAA;;wBAA9B,SAAS,GAAG,SAAkB;wBACpC,IAAI,CAAC,SAAS,EAAE;4BACd,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACK,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;wBACpC,IAAI,CAAC,GAAG,EAAE;4BACR,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACO,KAAK,GAAK,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,MAA7B,CAA6B;wBAC1C,IAAI,KAAK,EAAE;4BACT,sBAAO,KAAK,CAAC,SAAS,EAAA;yBACvB;wBACD,sBAAO,CAAC,CAAC,EAAA;;;;KACV;IAEK,sBAAQ,GAAd;;;gBACE,sBAAO,EAAE,EAAA;;;KACV;IAED,0BAAY,GAAZ,UAAa,KAAa,EAAE,MAAc,EAAE,SAAiB;QAC3D,IAAI,SAAS,GAAG,EAAE,EAAE;YAClB,OAAO,EAAE,CAAA;SACV;QAED,IAAM,IAAI,GAA2B,EAAE,CAAA;QACvC,IAAI,CAAC,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC5C,IAAI,CAAC,cAAc;YACjB,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACxE,IAAI,CAAC,MAAM,GACT,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAGnC,CAAC,IAAI,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACzB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,4CAAqC,IAAI,CAAC,WAAW,CAAE,CAAC,CAAA;SACzE;QACD,IAAI,CAAC,aAAa,GAAG;YACnB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QACzE,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,CAAC,MAAM,CACX,IAAI,EACJ,IAAI,CAAC,eAAe,CAClB,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CACF,CAAA;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,6BAAe,GAAf,UAAgB,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,IAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAM,WAAW,GAA8B,EAAE,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;gBAClB,IAAI,aAAa,GAAG,CAAC,EAAE;oBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;iBACjC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;aACf;SACF;QACD,OAAO,EAAE,WAAW,aAAA,EAAE,WAAW,aAAA,EAAE,CAAA;IACrC,CAAC;IAED,4BAA4B;IACtB,oBAAM,GAAZ,UAAa,IAA8B;;;;;;;wBACnC,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;wBACzD,qBAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAA;;wBAA9C,MAAM,GAAG,CAAC,SAAoC,CAAW;wBACjD,qBAAM,IAAA,uBAAK,EAAC,MAAM,CAAC;4BAEjC,0BAA0B;0BAFO;;wBAA3B,KAAK,GAAG,SAAmB;wBAEjC,0BAA0B;wBAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;4BACxC,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;yBACpB;6BAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;4BAC/C,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;yBACpB;6BAAM;4BACL,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;4BACjC,oDAAoD;yBACrD;wBAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACjC,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;wBACrD,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;wBACvC,IAAI,SAAS,EAAE;4BACb,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,EAAE,SAAS,CAAC,CAAC,CAAA;yBAC7D;wBACD,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;wBAEjD,+CAA+C;wBAC/C,IAAI,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;wBACnC,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;wBAC1B,CAAC,GAAG,CAAC;;;6BAAE,CAAA,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAA;wBAC/B,qBAAM,IAAA,sBAAe,EAAC,IAAI,CAAC,MAAM,CAAC;4BAClC,oBAAoB;0BADc;;wBAAlC,SAAkC,CAAA;wBAE5B,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAC9C,UAAU,IAAI,CAAC,CAAA;wBACT,QAAQ,GAA+B,EAAE,CAAA;wBAC3C,KAAK,SAAA,CAAA;wBACT,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;4BAC9B,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;4BAC1C,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE;gCAC3B,yDAAyD;gCACzD,qCAAqC;gCACrC,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;gCAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;6BAClC;iCAAM;gCACC,OAAO,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UA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package/dist/htsget.js
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package/dist/htsget.js.map
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{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"
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|
+
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,mDAA8C;AAC9C,gCAA6B;AAE7B,yDAA6C;AAC7C,6BAAuC;AAWvC,SAAe,MAAM,CAAC,GAAsB,EAAE,IAAyB;;;;;;wBACzD,qBAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,UAAO,KAAkB;;;;;oCACvB,GAAG,GAAc,KAAK,IAAnB,EAAE,OAAO,GAAK,KAAK,QAAV,CAAU;yCAC1B,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAvB,wBAAuB;oCACzB,sBAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,EAAA;;oCAKvC,OAAO,GAAc,OAAO,QAArB,EAAK,IAAI,UAAK,OAAO,EAA9B,WAAoB,CAAF,CAAY;oCACxB,qBAAM,KAAK,CAAC,GAAG,wBACtB,IAAI,KACP,OAAO,wBAAO,IAAI,CAAC,OAAO,GAAK,IAAI,KACnC,EAAA;;oCAHI,QAAM,SAGV;oCACF,IAAI,CAAC,KAAG,CAAC,EAAE,EAAE;wCACX,MAAM,IAAI,KAAK,CAAC,0BAAmB,KAAG,CAAC,UAAU,CAAE,CAAC,CAAA;qCACrD;oCACM,KAAA,CAAA,KAAA,MAAM,CAAA,CAAC,IAAI,CAAA;oCAAC,qBAAM,KAAG,CAAC,WAAW,EAAE,EAAA;wCAA1C,sBAAO,cAAY,SAAuB,EAAC,EAAA;;;yBAE9C,CAAC,CACH,EAAA;;oBApBK,GAAG,GAAG,SAoBX;oBAEM,KAAA,CAAA,KAAA,MAAM,CAAA,CAAC,MAAM,CAAA;oBAAC,qBAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,UAAA,GAAG,IAAI,OAAA,IAAA,uBAAK,EAAC,GAAG,CAAC,EAAV,CAAU,CAAC,CAAC,EAAA;wBAAlE,sBAAO,cAAc,SAA6C,EAAC,EAAA;;;;CACpE;AAED;IAAwC,8BAAO;IAK7C,oBAAY,IAA0C;QAAtD;QACE,mCAAmC;QACnC,kBAAM,EAAE,aAAa,EAAE,GAAG,EAAE,aAAa,EAAE,GAAG,EAAE,CAAC,SAGlD;QAFC,KAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,KAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;;IAC7B,CAAC;IAEM,0CAAqB,GAA5B,UACE,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAIC;QAJD,qBAAA,EAAA;YACE,WAAW,EAAE,KAAK;YAClB,aAAa,EAAE,KAAK;YACpB,aAAa,EAAE,MAAM;SACtB;;;;;;wBAEK,IAAI,GAAG,UAAG,IAAI,CAAC,OAAO,cAAI,IAAI,CAAC,OAAO,CAAE,CAAA;wBACxC,GAAG,GAAG,UAAG,IAAI,4BAAkB,GAAG,oBAAU,GAAG,kBAAQ,GAAG,gBAAa,CAAA;wBACvE,KAAK,GAAG,IAAI,CAAC,UAAU,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;wBACtC,6BAAM,KAAK,CAAC,GAAG,eAAO,IAAI,EAAG,GAAA;;wBAAtC,MAAM,GAAG,SAA6B;wBAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;4BACd,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;yBACnC;wBACY,6BAAM,MAAM,CAAC,IAAI,EAAE,GAAA;;wBAA1B,IAAI,GAAG,SAAmB;wBAClB,6BAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAA;;wBAArD,KAAK,GAAG,SAA6C;wBACrD,KAAK,GAAG;4BACZ,MAAM,EAAE,KAAK;4BACb,KAAK,EAAE,EAAE,IAAI,EAAE,EAAE,YAAY,EAAE,CAAC,EAAE,EAAE;4BACpC,QAAQ;gCACN,OAAO,UAAG,GAAG,cAAI,GAAG,cAAI,GAAG,CAAE,CAAA;4BAC/B,CAAC;yBACF,CAAA;wBAED,sBAAA,SAAO,iBAAA,cAAA,IAAI,CAAC,mBAAmB;4BAC7B,aAAa;4BACb,CAAC,KAAK,CAAC,EACP,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA,CAAA,CAAA,EAAA;4BAPD,4CAAA,SAOC,IAAA;;wBAPD,SAOC,CAAA;;;;;KACF;IAED,YAAY;IACN,+BAAU,GAAhB,UAAiB,MAGhB;;;;gBACS,KAAK,GAAK,MAAM,MAAX,CAAW;gBAChB,MAAM,GAAgB,KAAK,OAArB,EAAS,EAAE,GAAK,KAAK,MAAV,CAAU;gBACnC,sBAAO,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,EAAA;;;KACvE;IAEK,8BAAS,GAAf,UAAgB,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;;;wBAC3B,GAAG,GAAG,UAAG,IAAI,CAAC,OAAO,cAAI,IAAI,CAAC,OAAO,mCAAgC,CAAA;wBAC5D,qBAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,EAAA;;wBAA/B,MAAM,GAAG,SAAsB;wBACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;4BACd,MAAM,IAAI,KAAK,CAAC,0BAAmB,MAAM,CAAC,UAAU,CAAE,CAAC,CAAA;yBACxD;wBACY,qBAAM,MAAM,CAAC,IAAI,EAAE,EAAA;;wBAA1B,IAAI,GAAG,SAAmB;wBAClB,qBAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,EAAA;;wBAA5C,KAAK,GAAG,SAAoC;wBAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,mBAAS,EAAE;4BACtC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;yBAClC;wBACK,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBAE9B,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;wBACnD,SAAS,GAAG,IAAA,qBAAe,EAAC,UAAU,CAAC,CAAA;wBAIvC,QAAQ,GAAa,EAAE,CAAA;wBACvB,QAAQ,GAA2B,EAAE,CAAA;wBACrC,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,UAAC,CAAkB,IAAK,OAAA,CAAC,CAAC,GAAG,KAAK,IAAI,EAAd,CAAc,CAAC,CAAA;wBACxE,OAAO,CAAC,OAAO,CAAC,UAAC,MAA8B,EAAE,KAAa;4BAC5D,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,UAAC,IAAgB;gCACnC,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;oCACrB,uBAAuB;oCACvB,IAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;oCAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;oCACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;iCAC1B;4BACH,CAAC,CAAC,CAAA;wBACJ,CAAC,CAAC,CAAA;wBACF,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;wBAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;wBAC1B,sBAAO,SAAS,EAAA;;;;KACjB;IACH,iBAAC;AAAD,CAAC,AA/FD,CAAwC,iBAAO,GA+F9C"}
|
package/dist/record.d.ts
CHANGED
|
@@ -30,12 +30,12 @@ export default class BamRecord {
|
|
|
30
30
|
strand(): 1 | -1;
|
|
31
31
|
multi_segment_next_segment_strand(): 1 | -1 | undefined;
|
|
32
32
|
name(): any;
|
|
33
|
-
_read_name():
|
|
33
|
+
_read_name(): string;
|
|
34
34
|
/**
|
|
35
35
|
* Get the value of a tag, parsing the tags as far as necessary.
|
|
36
36
|
* Only called if we have not already parsed that field.
|
|
37
37
|
*/
|
|
38
|
-
_parseTag(tagName?: string):
|
|
38
|
+
_parseTag(tagName?: string): string | number | undefined;
|
|
39
39
|
_parseAllTags(): void;
|
|
40
40
|
_parseCigar(cigar: string): (string | number)[][];
|
|
41
41
|
/**
|
|
@@ -76,12 +76,12 @@ export default class BamRecord {
|
|
|
76
76
|
getReadBases(): string;
|
|
77
77
|
seq(): string;
|
|
78
78
|
getPairOrientation(): string | null;
|
|
79
|
-
_bin_mq_nl():
|
|
80
|
-
_flag_nc():
|
|
81
|
-
seq_length():
|
|
82
|
-
_next_refid():
|
|
83
|
-
_next_pos():
|
|
84
|
-
template_length():
|
|
79
|
+
_bin_mq_nl(): number;
|
|
80
|
+
_flag_nc(): number;
|
|
81
|
+
seq_length(): number;
|
|
82
|
+
_next_refid(): number;
|
|
83
|
+
_next_pos(): number;
|
|
84
|
+
template_length(): number;
|
|
85
85
|
toJSON(): {
|
|
86
86
|
[key: string]: any;
|
|
87
87
|
};
|
package/dist/record.js
CHANGED
|
@@ -5,24 +5,21 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
/* eslint-disable @typescript-eslint/no-empty-function */
|
|
7
7
|
var constants_1 = __importDefault(require("./constants"));
|
|
8
|
-
var SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('')
|
|
8
|
+
var SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
|
|
9
9
|
var CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
|
|
10
10
|
/**
|
|
11
11
|
* Class of each BAM record returned by this API.
|
|
12
12
|
*/
|
|
13
13
|
var BamRecord = /** @class */ (function () {
|
|
14
14
|
function BamRecord(args) {
|
|
15
|
-
this.
|
|
15
|
+
this.data = {};
|
|
16
16
|
this._tagList = [];
|
|
17
17
|
this._allTagsParsed = false;
|
|
18
|
+
var bytes = args.bytes, fileOffset = args.fileOffset;
|
|
19
|
+
var byteArray = bytes.byteArray, start = bytes.start;
|
|
18
20
|
this.data = {};
|
|
19
|
-
this.bytes =
|
|
20
|
-
|
|
21
|
-
end: args.bytes.end,
|
|
22
|
-
byteArray: args.bytes.byteArray,
|
|
23
|
-
};
|
|
24
|
-
this._id = args.fileOffset;
|
|
25
|
-
var _a = this.bytes, start = _a.start, byteArray = _a.byteArray;
|
|
21
|
+
this.bytes = bytes;
|
|
22
|
+
this._id = fileOffset;
|
|
26
23
|
this._refID = byteArray.readInt32LE(start + 4);
|
|
27
24
|
this.data.start = byteArray.readInt32LE(start + 8);
|
|
28
25
|
this.flags = (byteArray.readInt32LE(start + 16) & 0xffff0000) >> 16;
|
|
@@ -41,8 +38,7 @@ var BamRecord = /** @class */ (function () {
|
|
|
41
38
|
return this._get(field.toLowerCase());
|
|
42
39
|
};
|
|
43
40
|
BamRecord.prototype.end = function () {
|
|
44
|
-
return
|
|
45
|
-
(this.get('length_on_ref') || this.get('seq_length') || undefined));
|
|
41
|
+
return this.get('start') + this.get('length_on_ref');
|
|
46
42
|
};
|
|
47
43
|
BamRecord.prototype.seq_id = function () {
|
|
48
44
|
return this._refID;
|
|
@@ -73,7 +69,7 @@ var BamRecord = /** @class */ (function () {
|
|
|
73
69
|
}
|
|
74
70
|
});
|
|
75
71
|
var seen = {};
|
|
76
|
-
|
|
72
|
+
return tags.filter(function (t) {
|
|
77
73
|
if ((t in _this.data && _this.data[t] === undefined) ||
|
|
78
74
|
t === 'CG' ||
|
|
79
75
|
t === 'cg') {
|
|
@@ -84,7 +80,6 @@ var BamRecord = /** @class */ (function () {
|
|
|
84
80
|
seen[lt] = true;
|
|
85
81
|
return !s;
|
|
86
82
|
});
|
|
87
|
-
return tags;
|
|
88
83
|
};
|
|
89
84
|
BamRecord.prototype.parent = function () {
|
|
90
85
|
return undefined;
|
|
@@ -114,18 +109,14 @@ var BamRecord = /** @class */ (function () {
|
|
|
114
109
|
if (this.isSegmentUnmapped()) {
|
|
115
110
|
return undefined;
|
|
116
111
|
}
|
|
117
|
-
var
|
|
118
|
-
var p =
|
|
112
|
+
var _a = this.bytes, start = _a.start, byteArray = _a.byteArray;
|
|
113
|
+
var p = start +
|
|
119
114
|
36 +
|
|
120
115
|
this.get('_l_read_name') +
|
|
121
116
|
this.get('_n_cigar_op') * 4 +
|
|
122
117
|
this.get('_seq_bytes');
|
|
123
118
|
var lseq = this.get('seq_length');
|
|
124
|
-
|
|
125
|
-
for (var j = 0; j < lseq; ++j) {
|
|
126
|
-
qseq[j] = byteArray[p + j];
|
|
127
|
-
}
|
|
128
|
-
return qseq;
|
|
119
|
+
return byteArray.subarray(p, p + lseq);
|
|
129
120
|
};
|
|
130
121
|
BamRecord.prototype.strand = function () {
|
|
131
122
|
return this.isReverseComplemented() ? -1 : 1;
|
|
@@ -141,7 +132,8 @@ var BamRecord = /** @class */ (function () {
|
|
|
141
132
|
};
|
|
142
133
|
BamRecord.prototype._read_name = function () {
|
|
143
134
|
var nl = this.get('_l_read_name');
|
|
144
|
-
|
|
135
|
+
var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
|
|
136
|
+
return byteArray.toString('ascii', start + 36, start + 36 + nl - 1);
|
|
145
137
|
};
|
|
146
138
|
/**
|
|
147
139
|
* Get the value of a tag, parsing the tags as far as necessary.
|
|
@@ -154,9 +146,9 @@ var BamRecord = /** @class */ (function () {
|
|
|
154
146
|
if (this._allTagsParsed) {
|
|
155
147
|
return undefined;
|
|
156
148
|
}
|
|
157
|
-
var
|
|
149
|
+
var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
|
|
158
150
|
var p = this._tagOffset ||
|
|
159
|
-
|
|
151
|
+
start +
|
|
160
152
|
36 +
|
|
161
153
|
this.get('_l_read_name') +
|
|
162
154
|
this.get('_n_cigar_op') * 4 +
|
|
@@ -432,9 +424,13 @@ var BamRecord = /** @class */ (function () {
|
|
|
432
424
|
};
|
|
433
425
|
BamRecord.prototype._flags = function () { };
|
|
434
426
|
BamRecord.prototype.length_on_ref = function () {
|
|
435
|
-
this.
|
|
436
|
-
|
|
437
|
-
|
|
427
|
+
if (this.data.length_on_ref) {
|
|
428
|
+
return this.data.length_on_ref;
|
|
429
|
+
}
|
|
430
|
+
else {
|
|
431
|
+
this.get('cigar'); // the length_on_ref is set as a side effect
|
|
432
|
+
return this.data.length_on_ref;
|
|
433
|
+
}
|
|
438
434
|
};
|
|
439
435
|
BamRecord.prototype._n_cigar_op = function () {
|
|
440
436
|
return this.get('_flag_nc') & 0xffff;
|
|
@@ -452,21 +448,18 @@ var BamRecord = /** @class */ (function () {
|
|
|
452
448
|
return this.seq();
|
|
453
449
|
};
|
|
454
450
|
BamRecord.prototype.seq = function () {
|
|
455
|
-
var
|
|
456
|
-
var p = this.
|
|
457
|
-
36 +
|
|
458
|
-
this.get('_l_read_name') +
|
|
459
|
-
this.get('_n_cigar_op') * 4;
|
|
451
|
+
var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
|
|
452
|
+
var p = start + 36 + this.get('_l_read_name') + this.get('_n_cigar_op') * 4;
|
|
460
453
|
var seqBytes = this.get('_seq_bytes');
|
|
461
454
|
var len = this.get('seq_length');
|
|
462
455
|
var buf = '';
|
|
463
456
|
var i = 0;
|
|
464
457
|
for (var j = 0; j < seqBytes; ++j) {
|
|
465
458
|
var sb = byteArray[p + j];
|
|
466
|
-
buf +=
|
|
459
|
+
buf += SEQRET_DECODER[(sb & 0xf0) >> 4];
|
|
467
460
|
i++;
|
|
468
461
|
if (i < len) {
|
|
469
|
-
buf +=
|
|
462
|
+
buf += SEQRET_DECODER[sb & 0x0f];
|
|
470
463
|
i++;
|
|
471
464
|
}
|
|
472
465
|
}
|
package/dist/record.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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|
package/esm/bai.d.ts
CHANGED
|
@@ -9,7 +9,7 @@ export default class BAI extends IndexFile {
|
|
|
9
9
|
};
|
|
10
10
|
lineCount(refId: number, opts?: BaseOpts): Promise<any>;
|
|
11
11
|
fetchBai(opts?: BaseOpts): Promise<Buffer>;
|
|
12
|
-
_parse(
|
|
12
|
+
_parse(): Promise<{
|
|
13
13
|
[key: string]: any;
|
|
14
14
|
}>;
|
|
15
15
|
indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<{
|
package/esm/bai.js
CHANGED
|
@@ -2,7 +2,7 @@ import Long from 'long';
|
|
|
2
2
|
import { fromBytes } from './virtualOffset';
|
|
3
3
|
import Chunk from './chunk';
|
|
4
4
|
import IndexFile from './indexFile';
|
|
5
|
-
import { longToNumber,
|
|
5
|
+
import { longToNumber, optimizeChunks } from './util';
|
|
6
6
|
const BAI_MAGIC = 21578050; // BAI\1
|
|
7
7
|
function roundDown(n, multiple) {
|
|
8
8
|
return n - (n % multiple);
|
|
@@ -34,7 +34,7 @@ export default class BAI extends IndexFile {
|
|
|
34
34
|
return this.baiP;
|
|
35
35
|
}
|
|
36
36
|
// fetch and parse the index
|
|
37
|
-
async _parse(
|
|
37
|
+
async _parse() {
|
|
38
38
|
const data = { bai: true, maxBlockSize: 1 << 16 };
|
|
39
39
|
const bytes = await this.fetchBai();
|
|
40
40
|
// check BAI magic numbers
|
|
@@ -48,7 +48,6 @@ export default class BAI extends IndexFile {
|
|
|
48
48
|
data.indices = new Array(data.refCount);
|
|
49
49
|
let currOffset = 8;
|
|
50
50
|
for (let i = 0; i < data.refCount; i += 1) {
|
|
51
|
-
await abortBreakPoint(opts.signal);
|
|
52
51
|
// the binning index
|
|
53
52
|
const binCount = bytes.readInt32LE(currOffset);
|
|
54
53
|
let stats;
|
package/esm/bai.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,MAAM,CAAA;AACvB,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC3C,OAAO,KAAK,MAAM,SAAS,CAAA;AAE3B,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,EAAE,YAAY,EAAE,
|
|
1
|
+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,MAAM,CAAA;AACvB,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC3C,OAAO,KAAK,MAAM,SAAS,CAAA;AAE3B,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,EAAE,YAAY,EAAE,cAAc,EAAY,MAAM,QAAQ,CAAA;AAE/D,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;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAGxC,cAAc,CAAC,KAAa,EAAE,MAAc;QAC1C,MAAM,SAAS,GAAG,YAAY,CAC5B,IAAI,CAAC,WAAW,CACd,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,CAAC,EAC3D,IAAI,CACL,CACF,CAAA;QACD,OAAO,EAAE,SAAS,EAAE,CAAA;IACtB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;QAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACnC,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACjC,IAAI,CAAC,KAAK,EAAE;YACV,OAAO,CAAC,CAAC,CAAA;SACV;QACD,MAAM,GAAG,GAAG,KAAK,CAAC,KAAK,IAAI,EAAE,CAAA;QAC7B,OAAO,GAAG,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAA;IACzD,CAAC;IAED,QAAQ,CAAC,OAAiB,EAAE;QAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE;YACd,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACnD,IAAI,CAAC,IAAI,GAAG,SAAS,CAAA;gBACrB,MAAM,CAAC,CAAA;YACT,CAAC,CAAoB,CAAA;SACtB;QACD,OAAO,IAAI,CAAC,IAAI,CAAA;IAClB,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM;QACV,MAAM,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;QACzE,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAEnC,0BAA0B;QAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;YACvC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;SAClC;QAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACpC,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,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QACvC,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;YACzC,oBAAoB;YACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YAC9C,IAAI,KAAK,CAAA;YAET,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA+B,EAAE,CAAA;YAC/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;gBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;gBAC1C,UAAU,IAAI,CAAC,CAAA;gBACf,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE;oBACxB,UAAU,IAAI,CAAC,CAAA;oBACf,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oBAC9C,UAAU,IAAI,EAAE,CAAA;iBACjB;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE;oBAC7B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;iBACpE;qBAAM;oBACL,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;oBAChD,UAAU,IAAI,CAAC,CAAA;oBACf,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;oBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE;wBACtC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAC1C,UAAU,IAAI,EAAE,CAAA;wBAChB,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,CAAC,CAAC,CAAA;wBAC5B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;qBACjC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;iBACvB;aACF;YAED,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YACjD,UAAU,IAAI,CAAC,CAAA;YACf,sDAAsD;YACtD,oDAAoD;YACpD,qCAAqC;YACrC,MAAM,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;YAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE;gBACvC,WAAW,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;gBAC7C,UAAU,IAAI,CAAC,CAAA;gBACf,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;aAC1C;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;SACnD;QAED,OAAO,IAAI,CAAA;IACb,CAAC;IAED,KAAK,CAAC,QAAQ,CACZ,KAAa,EACb,KAAc,EACd,GAAY,EACZ,OAAiB,EAAE;QAEnB,MAAM,CAAC,GAAG,KAAK,CAAA;QACf,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;QACvC,IAAI,CAAC,MAAM,EAAE;YACX,OAAO,EAAE,CAAA;SACV;QACD,MAAM,EAAE,WAAW,GAAG,EAAE,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;QAC1C,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;YACvB,OAAO,EAAE,CAAA;SACV;QACD,MAAM,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC5E,MAAM,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACvD,IAAI,MAAM,CAAA;QACV,IAAI,KAAK,EAAE;YACT,MAAM,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;SAChC;aAAM;YACL,MAAM,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;SAC3C;QACD,MAAM,SAAS,GAAG,WAAW,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;QACnE,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE;YACpC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;SAC1D;QACD,IAAI,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE;YAC9C,MAAM,CAAC,CAAC,CAAC,GAAG;gBACV,KAAK,EAAE,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,GAAG,UAAU;gBACpD,KAAK,EAAE,CAAC,GAAG,CAAC;gBACZ,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC;aACf,CAAA;YACD,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;SAC9C;QACD,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YACpB,OAAO,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,KAAK,CAAC,SAAS,CAAC,GAAG,SAAS,EAAE,CAAA;QACjE,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;OAGG;IACH,QAAQ,CAAC,GAAW,EAAE,GAAW;QAC/B,GAAG,IAAI,CAAC,CAAA;QACR,OAAO;YACL,CAAC,CAAC,EAAE,CAAC,CAAC;YACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;SACzC,CAAA;IACH,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;QAEnB,IAAI,GAAG,GAAG,CAAC,EAAE;YACX,GAAG,GAAG,CAAC,CAAA;SACR;QAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,IAAI,CAAC,SAAS,EAAE;YACd,OAAO,EAAE,CAAA;SACV;QACD,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACnC,IAAI,CAAC,EAAE,EAAE;YACP,OAAO,EAAE,CAAA;SACV;QAED,uCAAuC;QACvC,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAC/C,MAAM,MAAM,GAAY,EAAE,CAAA;QAE1B,sEAAsE;QACtE,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE;YAC1C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE;gBACvC,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE;oBACpB,MAAM,SAAS,GAAG,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;oBAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;wBACzC,MAAM,CAAC,IAAI,CAAC,IAAI,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;qBAClE;iBACF;aACF;SACF;QAED,0EAA0E;QAC1E,mCAAmC;QACnC,MAAM,KAAK,GAAG,EAAE,CAAC,WAAW,CAAC,MAAM,CAAA;QACnC,IAAI,MAAM,GAAG,IAAI,CAAA;QACjB,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;QAC7C,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;QAC7C,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,IAAI,MAAM,EAAE,EAAE,CAAC,EAAE;YACrC,MAAM,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YAC5B,IAAI,EAAE,EAAE;gBACN,IAAI,CAAC,MAAM,IAAI,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE;oBACvC,MAAM,GAAG,EAAE,CAAA;iBACZ;aACF;SACF;QAED,OAAO,cAAc,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;IACvC,CAAC;CACF"}
|
package/esm/bamFile.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
/// <reference types="node" />
|
|
2
|
-
import Chunk from './chunk';
|
|
3
2
|
import { GenericFilehandle } from 'generic-filehandle';
|
|
3
|
+
import Chunk from './chunk';
|
|
4
4
|
import BAMFeature from './record';
|
|
5
5
|
import { BamOpts, BaseOpts } from './util';
|
|
6
6
|
export declare const BAM_MAGIC = 21840194;
|
|
@@ -14,6 +14,7 @@ export default class BamFile {
|
|
|
14
14
|
protected chrToIndex: any;
|
|
15
15
|
protected indexToChr: any;
|
|
16
16
|
private yieldThreadTime;
|
|
17
|
+
private featureCache;
|
|
17
18
|
/**
|
|
18
19
|
* @param {object} args
|
|
19
20
|
* @param {string} [args.bamPath]
|
|
@@ -56,7 +57,7 @@ export default class BamFile {
|
|
|
56
57
|
getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<BAMFeature[]>;
|
|
57
58
|
streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
|
|
58
59
|
_fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
|
|
59
|
-
fetchPairs(chrId: number,
|
|
60
|
+
fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts): Promise<BAMFeature[]>;
|
|
60
61
|
_readChunk({ chunk, opts }: {
|
|
61
62
|
chunk: Chunk;
|
|
62
63
|
opts: BaseOpts;
|