@gmod/cram 1.7.4 → 2.0.1
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 +9 -2
- package/README.md +343 -24
- package/dist/craiIndex.js.map +1 -1
- package/dist/cram-bundle.js +1 -1
- package/dist/cram-bundle.js.LICENSE.txt +6 -0
- package/dist/cramFile/codecs/beta.js.map +1 -1
- package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
- package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
- package/dist/cramFile/codecs/external.js.map +1 -1
- package/dist/cramFile/codecs/gamma.js.map +1 -1
- package/dist/cramFile/codecs/getBits.js.map +1 -1
- package/dist/cramFile/codecs/huffman.js.map +1 -1
- package/dist/cramFile/codecs/index.js.map +1 -1
- package/dist/cramFile/codecs/subexp.js.map +1 -1
- package/dist/cramFile/container/compressionScheme.js.map +1 -1
- package/dist/cramFile/container/index.js.map +1 -1
- package/dist/cramFile/file.d.ts +10 -3
- package/dist/cramFile/file.js +56 -50
- package/dist/cramFile/file.js.map +1 -1
- package/dist/cramFile/record.js.map +1 -1
- package/dist/cramFile/sectionParsers.d.ts +1 -0
- package/dist/cramFile/sectionParsers.js +7 -7
- package/dist/cramFile/sectionParsers.js.map +1 -1
- package/dist/cramFile/slice/decodeRecord.js +1 -1
- package/dist/cramFile/slice/decodeRecord.js.map +1 -1
- package/dist/cramFile/slice/index.js.map +1 -1
- package/dist/cramFile/util.d.ts +1 -0
- package/dist/cramFile/util.js.map +1 -1
- package/dist/indexedCramFile.js.map +1 -1
- package/dist/io/index.js.map +1 -1
- package/dist/rans/constants.d.ts +4 -3
- package/dist/rans/constants.js.map +1 -1
- package/dist/rans/d04.js +1 -0
- package/dist/rans/d04.js.map +1 -1
- package/dist/rans/d14.js +1 -0
- package/dist/rans/d14.js.map +1 -1
- package/dist/rans/decoding.d.ts +16 -19
- package/dist/rans/decoding.js +1 -0
- package/dist/rans/decoding.js.map +1 -1
- package/dist/rans/frequencies.d.ts +2 -2
- package/dist/rans/frequencies.js +1 -0
- package/dist/rans/frequencies.js.map +1 -1
- package/dist/rans/index.js +1 -0
- package/dist/rans/index.js.map +1 -1
- package/dist/sam.d.ts +5 -6
- package/dist/sam.js +23 -7
- package/dist/sam.js.map +1 -1
- package/dist/typescript.js.map +1 -1
- package/dist/unzip.d.ts +1 -0
- package/esm/craiIndex.js.map +1 -1
- package/esm/cramFile/codecs/beta.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
- package/esm/cramFile/codecs/external.js.map +1 -1
- package/esm/cramFile/codecs/gamma.js.map +1 -1
- package/esm/cramFile/codecs/getBits.js.map +1 -1
- package/esm/cramFile/codecs/huffman.js.map +1 -1
- package/esm/cramFile/codecs/index.js.map +1 -1
- package/esm/cramFile/codecs/subexp.js.map +1 -1
- package/esm/cramFile/container/compressionScheme.js.map +1 -1
- package/esm/cramFile/container/index.js.map +1 -1
- package/esm/cramFile/file.d.ts +10 -3
- package/esm/cramFile/file.js +17 -13
- package/esm/cramFile/file.js.map +1 -1
- package/esm/cramFile/record.js.map +1 -1
- package/esm/cramFile/sectionParsers.d.ts +1 -0
- package/esm/cramFile/sectionParsers.js +7 -7
- package/esm/cramFile/sectionParsers.js.map +1 -1
- package/esm/cramFile/slice/decodeRecord.js +1 -1
- package/esm/cramFile/slice/decodeRecord.js.map +1 -1
- package/esm/cramFile/slice/index.js.map +1 -1
- package/esm/cramFile/util.d.ts +1 -0
- package/esm/cramFile/util.js.map +1 -1
- package/esm/indexedCramFile.js.map +1 -1
- package/esm/io/index.js.map +1 -1
- package/esm/rans/constants.d.ts +4 -3
- package/esm/rans/constants.js.map +1 -1
- package/esm/rans/d04.js +1 -0
- package/esm/rans/d04.js.map +1 -1
- package/esm/rans/d14.js +1 -0
- package/esm/rans/d14.js.map +1 -1
- package/esm/rans/decoding.d.ts +16 -19
- package/esm/rans/decoding.js +1 -0
- package/esm/rans/decoding.js.map +1 -1
- package/esm/rans/frequencies.d.ts +2 -2
- package/esm/rans/frequencies.js +1 -0
- package/esm/rans/frequencies.js.map +1 -1
- package/esm/rans/index.js +1 -0
- package/esm/rans/index.js.map +1 -1
- package/esm/sam.d.ts +5 -6
- package/esm/sam.js +23 -7
- package/esm/sam.js.map +1 -1
- package/esm/typescript.js.map +1 -1
- package/esm/unzip.d.ts +1 -0
- package/package.json +11 -10
- package/src/cramFile/container/index.ts +4 -1
- package/src/cramFile/file.ts +23 -19
- package/src/rans/{d04.js → d04.ts} +1 -0
- package/src/rans/{d14.js → d14.ts} +1 -0
- package/src/rans/{decoding.js → decoding.ts} +1 -0
- package/src/rans/{frequencies.js → frequencies.ts} +1 -0
- package/src/rans/{index.js → index.ts} +1 -0
- package/src/sam.ts +30 -14
- /package/src/rans/{constants.js → constants.ts} +0 -0
package/esm/rans/d14.js
CHANGED
package/esm/rans/d14.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"d14.js","sourceRoot":"","sources":["../../src/rans/d14.
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{"version":3,"file":"d14.js","sourceRoot":"","sources":["../../src/rans/d14.ts"],"names":[],"mappings":"AAAA,aAAa;AACb,OAAO,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAA;AACtC,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,MAAM,CAAC,OAAO,UAAU,UAAU;AAChC,gBAAgB,CAAC,KAAK;AACtB,gBAAgB,CAAC,MAAM;AACvB,2BAA2B,CAAC,CAAC;AAC7B,yBAAyB,CAAC,IAAI;IAE9B,MAAM,SAAS,CAAC,UAAU,GAAG,MAAM,CAAC,SAAS,EAAE,CAAA;IAC/C,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAE1B,MAAM,SAAS,CAAC,IAAI,GAAG,UAAU,IAAI,CAAC,CAAA;IACtC,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,IAAI,CAAA;IACvB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,CAAA;IAC3B,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,CAAA;IAC3B,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,OAAO,EAAE,GAAG,IAAI,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC;QACrD,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAElE,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QAEpB,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QAEjE,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAE1C,EAAE,GAAG,EAAE,CAAA;QACP,EAAE,GAAG,EAAE,CAAA;QACP,EAAE,GAAG,EAAE,CAAA;QACP,EAAE,GAAG,EAAE,CAAA;IACT,CAAC;IAED,YAAY;IACZ,OAAO,EAAE,GAAG,UAAU,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC;QAChC,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,KAAK,GAAG,QAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACpE,EAAE,GAAG,EAAE,CAAA;IACT,CAAC;AACH,CAAC"}
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package/esm/rans/decoding.d.ts
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export default Decode;
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declare namespace Decode {
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export { FC };
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export { AriDecoder };
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export { Symbol };
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export { symbolInit };
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export { advanceStep };
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export { advanceSymbolStep };
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export { get };
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export { advanceSymbol };
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export { renormalize };
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}
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declare class FC {
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C: any;
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constructor();
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}
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declare class AriDecoder {
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R: any;
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constructor();
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declare class Symbol {
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freq: any;
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constructor();
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declare function symbolInit(sym: any, start: any, freq: any): void;
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declare function advanceStep(r: any, start: any, freq: any, scaleBits: any): number;
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declare function advanceSymbolStep(r: any, sym: any, scaleBits: any): number;
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declare function get(r: any, scaleBits: any): number;
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declare function get(/* final int */ r: any, /* final int */ scaleBits: any): number;
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declare function advanceSymbol(r: any, pptr: any, sym: any, scaleBits: any): any;
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declare function renormalize(r: any, pptr: any): any;
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declare const Decode: {
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FC: typeof FC;
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AriDecoder: typeof AriDecoder;
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Symbol: typeof Symbol;
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symbolInit: typeof symbolInit;
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advanceStep: typeof advanceStep;
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advanceSymbolStep: typeof advanceSymbolStep;
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get: typeof get;
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advanceSymbol: typeof advanceSymbol;
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renormalize: typeof renormalize;
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};
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export default Decode;
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package/esm/rans/decoding.js
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package/esm/rans/decoding.js.map
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{"version":3,"file":"decoding.js","sourceRoot":"","sources":["../../src/rans/decoding.
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{"version":3,"file":"decoding.js","sourceRoot":"","sources":["../../src/rans/decoding.ts"],"names":[],"mappings":"AAAA,aAAa;AACb,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,EAAE,WAAW,EAAE,MAAM,aAAa,CAAA;AAEzC,MAAM,EAAE;IACN,YAAY;IACZ;QACE,IAAI,CAAC,CAAC,GAAG,SAAS,CAAA;QAClB,IAAI,CAAC,CAAC,GAAG,SAAS,CAAA;IACpB,CAAC;CACF;AAED,MAAM,UAAU;IACd,+BAA+B;IAC/B,YAAY;IAEZ;QACE,IAAI,CAAC,EAAE,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,EAAE,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC3C,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,EAAE,EAAE,CAAA;QACvB,CAAC;QACD,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;IACf,CAAC;CACF;AAED,MAAM,MAAM;IACV,gCAAgC;IAChC,iCAAiC;IACjC;QACE,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;QACtB,IAAI,CAAC,IAAI,GAAG,SAAS,CAAA;IACvB,CAAC;CACF;AAED,oEAAoE;AACpE,SAAS,UAAU,CAAC,GAAG,EAAE,KAAK,EAAE,IAAI;IAClC,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,IAAI,EAAE,CAAC,EAAE,CAAC;QACxB,MAAM,IAAI,kBAAkB,CAAC,kCAAkC,CAAC,CAAA;IAClE,CAAC;IACD,IAAI,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,KAAK,CAAC,EAAE,CAAC;QACjC,MAAM,IAAI,kBAAkB,CAAC,iCAAiC,CAAC,CAAA;IACjE,CAAC;IACD,GAAG,CAAC,KAAK,GAAG,KAAK,CAAA;IACjB,GAAG,CAAC,IAAI,GAAG,IAAI,CAAA;AACjB,CAAC;AAED,2EAA2E;AAC3E,sEAAsE;AACtE,oBAAoB;AACpB,wCAAwC;AACxC,wBAAwB,CAAC,SAAS,WAAW;AAC3C,eAAe,CAAC,CAAC;AACjB,eAAe,CAAC,KAAK;AACrB,eAAe,CAAC,IAAI;AACpB,eAAe,CAAC,SAAS;IAEzB,eAAe,CAAC,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAA;IAEjD,cAAc;IACd,OAAO,IAAI,GAAG,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,KAAK,CAAA;AACrD,CAAC;AAED,wDAAwD;AACxD,iBAAiB,CAAC,SAAS,iBAAiB;AAC1C,eAAe,CAAC,CAAC;AACjB,yBAAyB,CAAC,GAAG;AAC7B,eAAe,CAAC,SAAS;IAEzB,OAAO,WAAW,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;AACvD,CAAC;AAED,0EAA0E;AAC1E,gBAAgB,CAAC,SAAS,GAAG,CAAC,eAAe,CAAC,CAAC,EAAE,eAAe,CAAC,SAAS;IACxE,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAC,CAAA;AACnC,CAAC;AAED,2EAA2E;AAC3E,sEAAsE;AACtE,oBAAoB;AACpB,iEAAiE;AACjE,wBAAwB,CAAC,SAAS,OAAO;AACvC,SAAS,CAAC,CAAC;AACX,sBAAsB,CAAC,IAAI;AAC3B,eAAe,CAAC,KAAK;AACrB,eAAe,CAAC,IAAI;AACpB,eAAe,CAAC,SAAS;IAEzB,eAAe,CAAC,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAA;IAEjD,cAAc;IACd,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,KAAK,CAAA;IAEhD,eAAe;IACf,IAAI,CAAC,GAAG,WAAW,EAAE,CAAC;QACpB,GAAG,CAAC;YACF,eAAe,CAAC,MAAM,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,GAAG,EAAE,CAAA;YAC3C,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;QAClB,CAAC,QAAQ,CAAC,GAAG,WAAW,EAAC;IAC3B,CAAC;IAED,OAAO,CAAC,CAAA;AACV,CAAC;AAED,oDAAoD;AACpD,iBAAiB,CAAC,SAAS,aAAa;AACtC,eAAe,CAAC,CAAC;AACjB,sBAAsB,CAAC,IAAI;AAC3B,yBAAyB,CAAC,GAAG;AAC7B,eAAe,CAAC,SAAS;IAEzB,OAAO,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;AACzD,CAAC;AAED,gBAAgB;AAChB,iBAAiB,CAAC,SAAS,WAAW;AACpC,SAAS,CAAC,CAAC;AACX,sBAAsB,CAAC,IAAI;IAE3B,eAAe;IACf,IAAI,CAAC,GAAG,WAAW,EAAE,CAAC;QACpB,GAAG,CAAC;YACF,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,CAAA;QACpC,CAAC,QAAQ,CAAC,GAAG,WAAW,EAAC;IAC3B,CAAC;IAED,OAAO,CAAC,CAAA;AACV,CAAC;AAED,MAAM,MAAM,GAAG;IACb,EAAE;IACF,UAAU;IACV,MAAM;IACN,UAAU;IACV,WAAW;IACX,iBAAiB;IACjB,GAAG;IACH,aAAa;IACb,WAAW;CACZ,CAAA;AAED,eAAe,MAAM,CAAA"}
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export function readStatsO0(cp: any, decoder: any, syms: any): void;
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export function readStatsO1(cp: any, D: any, syms: any): void;
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export declare function readStatsO0(cp: any, decoder: any, syms: any): void;
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export declare function readStatsO1(cp: any, D: any, syms: any): void;
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package/esm/rans/frequencies.js
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{"version":3,"file":"frequencies.js","sourceRoot":"","sources":["../../src/rans/frequencies.
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|
+
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AI,IAAI,CAAC,CAAA;YACT,CAAC,IAAI,CAAC,CAAA;QACR,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;QACrB,CAAC;IACH,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAC;AACnB,CAAC"}
|
package/esm/rans/index.js
CHANGED
package/esm/rans/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/rans/index.
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/rans/index.ts"],"names":[],"mappings":"AAAA,aAAa;AACb,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,eAAe,CAAA;AAExD,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,GAAG,MAAM,OAAO,CAAA;AAEvB,wCAAwC;AACxC,6CAA6C;AAC7C,MAAM,SAAS,CAAC,eAAe,GAAG,CAAC,CAAA;AACnC,uCAAuC;AACvC,iEAAiE;AAEjE,eAAe;AACf,iBAAiB;AAEjB,oDAAoD;AACpD,gBAAgB;AAChB,4CAA4C;AAC5C,6DAA6D;AAC7D,0EAA0E;AAC1E,YAAY;AACZ,QAAQ;AACR,IAAI;AAEJ,gGAAgG;AAChG,kCAAkC;AAClC,+BAA+B;AAE/B,iCAAiC;AACjC,iDAAiD;AAEjD,uBAAuB;AACvB,qBAAqB;AACrB,qDAAqD;AACrD,oBAAoB;AACpB,qDAAqD;AAErD,mBAAmB;AACnB,0EAA0E;AAC1E,QAAQ;AACR,IAAI;AAEJ,oEAAoE;AACpE,+EAA+E;AAC/E,yFAAyF;AACzF,2BAA2B;AAC3B,sDAAsD;AACtD,gDAAgD;AAChD,mEAAmE;AACnE,8CAA8C;AAC9C,sBAAsB;AACtB,IAAI;AAEJ,+DAA+D;AAC/D,qEAAqE;AACrE,mDAAmD;AACnD,oDAAoD;AACpD,2DAA2D;AAC3D,wCAAwC;AAExC,gEAAgE;AAChE,gEAAgE;AAEhE,6CAA6C;AAC7C,oFAAoF;AAEpF,sBAAsB;AACtB,2EAA2E;AAE3E,mEAAmE;AACnE,oCAAoC;AACpC,sBAAsB;AACtB,IAAI;AAEJ,+DAA+D;AAC/D,qEAAqE;AACrE,mDAAmD;AACnD,oDAAoD;AACpD,2DAA2D;AAC3D,wCAAwC;AAExC,kEAAkE;AAClE,kEAAkE;AAElE,6CAA6C;AAC7C,oFAAoF;AAEpF,sBAAsB;AACtB,2EAA2E;AAE3E,mEAAmE;AACnE,oCAAoC;AACpC,sBAAsB;AACtB,IAAI;AAEJ,kFAAkF;AAClF,8IAA8I;AAC9I,6DAA6D;AAC7D,sCAAsC;AACtC,oCAAoC;AACpC,8CAA8C;AAC9C,gEAAgE;AAChE,+DAA+D;AAC/D,sCAAsC;AACtC,kFAAkF;AAClF,8CAA8C;AAC9C,wBAAwB;AACxB,IAAI;AAEJ,SAAiC,oBAAoB;AACnD,uBAAuB,CAAC,KAAK;AAC7B,uBAAuB,CAAC,GAAG;IAE3B,wCAAwC;IACxC,MAAM,CAAC,GAAG,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAA;IACnC,MAAM,IAAI,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACxC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,MAAM,EAAE,CAAA;IACjC,CAAC;IAED,WAAW,CAAC,KAAK,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,GAAG,CAAC,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,CAAC,CAAA;IAExB,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,SAAiC,oBAAoB;AACnD,sBAAsB,CAAC,KAAK;AAC5B,sBAAsB,CAAC,MAAM;IAE7B,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACrC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAA;IAClC,CAAC;IACD,MAAM,iCAAiC,CAAC,IAAI,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IAC7D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACxC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC3C,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,MAAM,EAAE,CAAA;QACpC,CAAC;IACH,CAAC;IACD,WAAW,CAAC,KAAK,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,GAAG,CAAC,KAAK,EAAE,MAAM,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,OAAO,MAAM,CAAA;AACf,CAAC;AAED,mEAAmE;AACnE,MAAM,UAAU;IACd,YAAY,UAAU,EAAE,oBAAoB,GAAG,CAAC;QAC9C,IAAI,CAAC,OAAO,GAAG,UAAU,CAAA;QACzB,IAAI,CAAC,SAAS,GAAG,oBAAoB,CAAA;QACrC,IAAI,CAAC,MAAM,GAAG,UAAU,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,GAAG;QACD,MAAM,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;QACtC,IAAI,CAAC,SAAS,IAAI,CAAC,CAAA;QACnB,OAAO,CAAC,CAAA;IACV,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,GAAG,EAAE,CAAA;IACnB,CAAC;IAED,SAAS,CAAC,QAAQ;QAChB,OAAO,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;IAC/B,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,GAAG,CAAC,GAAG;QACL,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,GAAG,CAAA;QAClC,IAAI,CAAC,SAAS,IAAI,CAAC,CAAA;QACnB,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,KAAK,CAAC,QAAQ,EAAE,GAAG;QACjB,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,GAAG,GAAG,CAAA;QAC5B,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,WAAW,CAAC,GAAG;QACb,IAAI,CAAC,SAAS,GAAG,GAAG,CAAA;QACpB,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,MAAM;QACJ,MAAM,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;QAClD,IAAI,CAAC,SAAS,IAAI,CAAC,CAAA;QACnB,OAAO,CAAC,CAAA;IACV,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,SAAS,CAAA;IAC7C,CAAC;CACF;AAED,uEAAuE;AACvE,MAAM,CAAC,OAAO,UAAU,UAAU,CAChC,WAAW,EACX,YAAY,EACZ,oBAAoB,GAAG,CAAC;IAExB,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC7B,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACpB,OAAO,YAAY,CAAA;IACrB,CAAC;IAED,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,WAAW,EAAE,oBAAoB,CAAC,CAAA;IAC/D,wCAAwC;IAExC,MAAM,KAAK,GAAG,KAAK,CAAC,GAAG,EAAE,CAAA;IACzB,IAAI,KAAK,KAAK,CAAC,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;QAC/B,MAAM,IAAI,kBAAkB,CAAC,sBAAsB,KAAK,EAAE,CAAC,CAAA;IAC7D,CAAC;IAED,MAAM,SAAS,CAAC,SAAS,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1C,IAAI,SAAS,KAAK,KAAK,CAAC,SAAS,EAAE,GAAG,eAAe,EAAE,CAAC;QACtD,MAAM,IAAI,kBAAkB,CAAC,yBAAyB,CAAC,CAAA;IACzD,CAAC;IAED,MAAM,SAAS,CAAC,UAAU,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC3C,MAAM,MAAM,GAAG,IAAI,UAAU,CAAC,YAAY,IAAI,MAAM,CAAC,WAAW,CAAC,UAAU,CAAC,CAAC,CAAA;IAC7E,gCAAgC;IAEhC,IAAI,MAAM,CAAC,MAAM,GAAG,UAAU,EAAE,CAAC;QAC/B,MAAM,IAAI,kBAAkB,CAC1B,kCAAkC,UAAU,SAAS,CACtD,CAAA;IACH,CAAC;IAED,QAAQ,KAAK,EAAE,CAAC;QACd,KAAK,CAAC;YACJ,OAAO,oBAAoB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAE5C,KAAK,CAAC;YACJ,OAAO,oBAAoB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAE5C;YACE,MAAM,IAAI,kBAAkB,CAAC,uBAAuB,KAAK,EAAE,CAAC,CAAA;IAChE,CAAC;AACH,CAAC"}
|
package/esm/sam.d.ts
CHANGED
|
@@ -1,8 +1,7 @@
|
|
|
1
|
-
export
|
|
1
|
+
export declare function parseHeaderText(text: string): {
|
|
2
2
|
tag: string;
|
|
3
|
-
data:
|
|
3
|
+
data: {
|
|
4
4
|
tag: string;
|
|
5
|
-
value: string;
|
|
6
|
-
}
|
|
7
|
-
};
|
|
8
|
-
export declare function parseHeaderText(text: string): HeaderDataItem[];
|
|
5
|
+
value: string | undefined;
|
|
6
|
+
}[];
|
|
7
|
+
}[];
|
package/esm/sam.js
CHANGED
|
@@ -1,16 +1,32 @@
|
|
|
1
1
|
export function parseHeaderText(text) {
|
|
2
2
|
const lines = text.split(/\r?\n/);
|
|
3
3
|
const data = [];
|
|
4
|
-
|
|
4
|
+
for (const line of lines) {
|
|
5
5
|
const [tag, ...fields] = line.split(/\t/);
|
|
6
|
-
const parsedFields = fields.map(f => {
|
|
7
|
-
const [fieldTag, value] = f.split(':', 2);
|
|
8
|
-
return { tag: fieldTag, value };
|
|
9
|
-
});
|
|
10
6
|
if (tag) {
|
|
11
|
-
data.push({
|
|
7
|
+
data.push({
|
|
8
|
+
tag: tag.slice(1),
|
|
9
|
+
data: fields.map(f => {
|
|
10
|
+
const r = f.indexOf(':');
|
|
11
|
+
if (r !== -1) {
|
|
12
|
+
return {
|
|
13
|
+
tag: f.slice(0, r),
|
|
14
|
+
value: f.slice(r + 1),
|
|
15
|
+
};
|
|
16
|
+
}
|
|
17
|
+
else {
|
|
18
|
+
// @CO lines are not comma separated.
|
|
19
|
+
// See "samtools view -H c2\#pad.3.0.cram"
|
|
20
|
+
// so, just store value tag itself
|
|
21
|
+
return {
|
|
22
|
+
tag: f,
|
|
23
|
+
value: undefined,
|
|
24
|
+
};
|
|
25
|
+
}
|
|
26
|
+
}),
|
|
27
|
+
});
|
|
12
28
|
}
|
|
13
|
-
}
|
|
29
|
+
}
|
|
14
30
|
return data;
|
|
15
31
|
}
|
|
16
32
|
//# sourceMappingURL=sam.js.map
|
package/esm/sam.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAMJ,EAAE,CAAA;IACR,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC;wBACb,OAAO;4BACL,GAAG,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC;4BAClB,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC;yBACtB,CAAA;oBACH,CAAC;yBAAM,CAAC;wBACN,qCAAqC;wBACrC,0CAA0C;wBAC1C,kCAAkC;wBAClC,OAAO;4BACL,GAAG,EAAE,CAAC;4BACN,KAAK,EAAE,SAAS;yBACjB,CAAA;oBACH,CAAC;gBACH,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
|
package/esm/typescript.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,gBAAgB,CAAI,CAAuB;IACzD,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,SAAS,EAAE;
|
|
1
|
+
{"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,gBAAgB,CAAI,CAAuB;IACzD,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;QAClC,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;IAC/C,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC"}
|
package/esm/unzip.d.ts
CHANGED
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/cram",
|
|
3
|
-
"version": "
|
|
3
|
+
"version": "2.0.1",
|
|
4
4
|
"description": "read CRAM files with pure Javascript",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/cram-js",
|
|
@@ -23,7 +23,7 @@
|
|
|
23
23
|
"scripts": {
|
|
24
24
|
"test": "jest",
|
|
25
25
|
"lint": "eslint src test",
|
|
26
|
-
"docs": "documentation readme --shallow src/indexedCramFile.
|
|
26
|
+
"docs": "documentation readme --shallow src/indexedCramFile.ts --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/craiIndex.ts --section=CraiIndex; documentation readme --shallow errors.ts '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/cramFile/record.ts --section=CramRecord",
|
|
27
27
|
"prebuild": "npm run clean",
|
|
28
28
|
"clean": "rimraf dist esm",
|
|
29
29
|
"build:esm": "tsc --target es2018 --outDir esm",
|
|
@@ -50,34 +50,35 @@
|
|
|
50
50
|
"long": "^4.0.0",
|
|
51
51
|
"md5": "^2.2.1",
|
|
52
52
|
"pako": "^1.0.4",
|
|
53
|
-
"quick-lru": "^4.0.1"
|
|
53
|
+
"quick-lru": "^4.0.1",
|
|
54
|
+
"xz-decompress": "^0.2.1"
|
|
54
55
|
},
|
|
55
56
|
"devDependencies": {
|
|
56
57
|
"@babel/plugin-transform-modules-commonjs": "^7.18.2",
|
|
57
58
|
"@babel/preset-typescript": "^7.17.12",
|
|
58
|
-
"@gmod/indexedfasta": "^2.0
|
|
59
|
+
"@gmod/indexedfasta": "^2.1.0",
|
|
59
60
|
"@types/buffer-crc32": "^0.2.2",
|
|
60
61
|
"@types/jest": "^29.2.4",
|
|
61
62
|
"@types/long": "^4.0.2",
|
|
62
63
|
"@types/md5": "^2.3.2",
|
|
63
64
|
"@types/pako": "^1.0.3",
|
|
64
|
-
"@typescript-eslint/eslint-plugin": "^
|
|
65
|
-
"@typescript-eslint/parser": "^
|
|
65
|
+
"@typescript-eslint/eslint-plugin": "^6.9.1",
|
|
66
|
+
"@typescript-eslint/parser": "^6.9.1",
|
|
66
67
|
"buffer": "^6.0.3",
|
|
67
68
|
"documentation": "^14.0.1",
|
|
68
69
|
"eslint": "^8.30.0",
|
|
69
|
-
"eslint-config-prettier": "^
|
|
70
|
+
"eslint-config-prettier": "^9.0.0",
|
|
70
71
|
"eslint-plugin-import": "^2.25.4",
|
|
71
|
-
"eslint-plugin-prettier": "^
|
|
72
|
+
"eslint-plugin-prettier": "^5.0.1",
|
|
72
73
|
"glob": "^10.3.1",
|
|
73
74
|
"jest": "^29.3.1",
|
|
74
75
|
"mock-fs": "^5.2.0",
|
|
75
|
-
"prettier": "^
|
|
76
|
+
"prettier": "^3.0.3",
|
|
76
77
|
"rimraf": "^5.0.1",
|
|
77
78
|
"ts-jest": "^29.0.3",
|
|
78
79
|
"typescript": "^5.0.3",
|
|
79
80
|
"url": "^0.11.0",
|
|
80
|
-
"webpack": "5.
|
|
81
|
+
"webpack": "^5.89.0",
|
|
81
82
|
"webpack-cli": "^5.0.1"
|
|
82
83
|
},
|
|
83
84
|
"publishConfig": {
|
|
@@ -6,7 +6,10 @@ import CramContainerCompressionScheme from './compressionScheme'
|
|
|
6
6
|
import CramFile from '../file'
|
|
7
7
|
|
|
8
8
|
export default class CramContainer {
|
|
9
|
-
constructor(
|
|
9
|
+
constructor(
|
|
10
|
+
public file: CramFile,
|
|
11
|
+
public filePosition: number,
|
|
12
|
+
) {}
|
|
10
13
|
|
|
11
14
|
// memoize
|
|
12
15
|
getHeader() {
|
package/src/cramFile/file.ts
CHANGED
|
@@ -1,9 +1,11 @@
|
|
|
1
1
|
import { unzip } from '../unzip'
|
|
2
2
|
import crc32 from 'buffer-crc32'
|
|
3
3
|
import QuickLRU from 'quick-lru'
|
|
4
|
+
import htscodecs from '@jkbonfield/htscodecs'
|
|
5
|
+
import { Parser } from '@gmod/binary-parser'
|
|
4
6
|
// @ts-expect-error
|
|
5
7
|
import bzip2 from 'bzip2'
|
|
6
|
-
|
|
8
|
+
import { XzReadableStream } from 'xz-decompress'
|
|
7
9
|
import { CramMalformedError, CramUnimplementedError } from '../errors'
|
|
8
10
|
import ransuncompress from '../rans'
|
|
9
11
|
import {
|
|
@@ -12,16 +14,24 @@ import {
|
|
|
12
14
|
cramFileDefinition as cramFileDefinitionParser,
|
|
13
15
|
getSectionParsers,
|
|
14
16
|
} from './sectionParsers'
|
|
15
|
-
|
|
17
|
+
|
|
16
18
|
import CramContainer from './container'
|
|
17
19
|
|
|
18
20
|
import { open } from '../io'
|
|
19
21
|
import { parseItem, tinyMemoize } from './util'
|
|
20
22
|
import { parseHeaderText } from '../sam'
|
|
21
|
-
import { Parser } from '@gmod/binary-parser'
|
|
22
23
|
import CramRecord from './record'
|
|
23
24
|
import { Filehandle } from './filehandle'
|
|
24
25
|
|
|
26
|
+
function bufferToStream(buf: Buffer) {
|
|
27
|
+
return new ReadableStream({
|
|
28
|
+
start(controller) {
|
|
29
|
+
controller.enqueue(buf)
|
|
30
|
+
controller.close()
|
|
31
|
+
},
|
|
32
|
+
})
|
|
33
|
+
}
|
|
34
|
+
|
|
25
35
|
//source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
|
|
26
36
|
function getEndianness() {
|
|
27
37
|
const uInt32 = new Uint32Array([0x11223344])
|
|
@@ -99,17 +109,6 @@ export default class CramFile {
|
|
|
99
109
|
}
|
|
100
110
|
}
|
|
101
111
|
|
|
102
|
-
// toString() {
|
|
103
|
-
// if (this.file.filename) {
|
|
104
|
-
// return this.file.filename
|
|
105
|
-
// }
|
|
106
|
-
// if (this.file.url) {
|
|
107
|
-
// return this.file.url
|
|
108
|
-
// }
|
|
109
|
-
//
|
|
110
|
-
// return '(cram file)'
|
|
111
|
-
// }
|
|
112
|
-
|
|
113
112
|
// can just read this object like a filehandle
|
|
114
113
|
read(
|
|
115
114
|
buffer: Buffer,
|
|
@@ -247,9 +246,8 @@ export default class CramFile {
|
|
|
247
246
|
let containerCount = 0
|
|
248
247
|
let position = sectionParsers.cramFileDefinition.maxLength
|
|
249
248
|
while (position + cramContainerHeader1.maxLength + 8 < fileSize) {
|
|
250
|
-
const currentHeader =
|
|
251
|
-
position
|
|
252
|
-
).getHeader()
|
|
249
|
+
const currentHeader =
|
|
250
|
+
await this.getContainerAtPosition(position).getHeader()
|
|
253
251
|
if (!currentHeader) {
|
|
254
252
|
break
|
|
255
253
|
}
|
|
@@ -319,7 +317,7 @@ export default class CramFile {
|
|
|
319
317
|
return data
|
|
320
318
|
}
|
|
321
319
|
|
|
322
|
-
_uncompress(
|
|
320
|
+
async _uncompress(
|
|
323
321
|
compressionMethod: CompressionMethod,
|
|
324
322
|
inputBuffer: Buffer,
|
|
325
323
|
outputBuffer: Buffer,
|
|
@@ -340,6 +338,12 @@ export default class CramFile {
|
|
|
340
338
|
size -= chunk.length
|
|
341
339
|
}
|
|
342
340
|
} while (chunk != -1)
|
|
341
|
+
} else if (compressionMethod === 'lzma') {
|
|
342
|
+
const decompressedResponse = new Response(
|
|
343
|
+
new XzReadableStream(bufferToStream(inputBuffer)),
|
|
344
|
+
)
|
|
345
|
+
const ret = Buffer.from(await decompressedResponse.arrayBuffer())
|
|
346
|
+
ret.copy(outputBuffer)
|
|
343
347
|
} else if (compressionMethod === 'rans') {
|
|
344
348
|
ransuncompress(inputBuffer, outputBuffer)
|
|
345
349
|
//htscodecs r4x8 is slower, but compatible.
|
|
@@ -386,7 +390,7 @@ export default class CramFile {
|
|
|
386
390
|
blockContentPosition,
|
|
387
391
|
)
|
|
388
392
|
|
|
389
|
-
this._uncompress(
|
|
393
|
+
await this._uncompress(
|
|
390
394
|
blockHeader.compressionMethod,
|
|
391
395
|
compressedData,
|
|
392
396
|
uncompressedData,
|
package/src/sam.ts
CHANGED
|
@@ -1,20 +1,36 @@
|
|
|
1
|
-
export
|
|
2
|
-
tag: string
|
|
3
|
-
data: Array<{ tag: string; value: string }>
|
|
4
|
-
}
|
|
5
|
-
|
|
6
|
-
export function parseHeaderText(text: string): HeaderDataItem[] {
|
|
1
|
+
export function parseHeaderText(text: string) {
|
|
7
2
|
const lines = text.split(/\r?\n/)
|
|
8
|
-
const data:
|
|
9
|
-
|
|
3
|
+
const data: {
|
|
4
|
+
tag: string
|
|
5
|
+
data: {
|
|
6
|
+
tag: string
|
|
7
|
+
value: string | undefined
|
|
8
|
+
}[]
|
|
9
|
+
}[] = []
|
|
10
|
+
for (const line of lines) {
|
|
10
11
|
const [tag, ...fields] = line.split(/\t/)
|
|
11
|
-
const parsedFields = fields.map(f => {
|
|
12
|
-
const [fieldTag, value] = f.split(':', 2)
|
|
13
|
-
return { tag: fieldTag, value }
|
|
14
|
-
})
|
|
15
12
|
if (tag) {
|
|
16
|
-
data.push({
|
|
13
|
+
data.push({
|
|
14
|
+
tag: tag.slice(1),
|
|
15
|
+
data: fields.map(f => {
|
|
16
|
+
const r = f.indexOf(':')
|
|
17
|
+
if (r !== -1) {
|
|
18
|
+
return {
|
|
19
|
+
tag: f.slice(0, r),
|
|
20
|
+
value: f.slice(r + 1),
|
|
21
|
+
}
|
|
22
|
+
} else {
|
|
23
|
+
// @CO lines are not comma separated.
|
|
24
|
+
// See "samtools view -H c2\#pad.3.0.cram"
|
|
25
|
+
// so, just store value tag itself
|
|
26
|
+
return {
|
|
27
|
+
tag: f,
|
|
28
|
+
value: undefined,
|
|
29
|
+
}
|
|
30
|
+
}
|
|
31
|
+
}),
|
|
32
|
+
})
|
|
17
33
|
}
|
|
18
|
-
}
|
|
34
|
+
}
|
|
19
35
|
return data
|
|
20
36
|
}
|
|
File without changes
|