@gmod/cram 2.0.0 → 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/dist/craiIndex.js.map +1 -1
- package/dist/cram-bundle.js +1 -1
- 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 +8 -1
- 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/d04.js.map +1 -1
- package/dist/rans/d14.js.map +1 -1
- package/dist/rans/decoding.js.map +1 -1
- package/dist/rans/frequencies.js.map +1 -1
- 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 +8 -1
- 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/d04.js.map +1 -1
- package/esm/rans/d14.js.map +1 -1
- package/esm/rans/decoding.js.map +1 -1
- package/esm/rans/frequencies.js.map +1 -1
- 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 +2 -2
- package/src/sam.ts +30 -14
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{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,SAAU,SAAQ,eAGtC;IACC,YAAY,UAAsC,EAAE,QAAe;QACjE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;
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{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,SAAU,SAAQ,eAGtC;IACC,YAAY,UAAsC,EAAE,QAAe;QACjE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,6CAA6C,CAC9D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,QAAQ,GAAG,IAAA,iBAAO,EACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,CAAA;QACD,OAAO,QAAQ,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IAC1C,CAAC;CACF;AA1BD,4BA0BC"}
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{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":";;;;;AAAA,kCAAqC;AAErC,oDAA4C;AAW5C,MAAqB,kBAAmB,SAAQ,eAG/C;IAGC,YACE,UAAiD,EACjD,QAAqB,EACrB,gBAAkC;QAElC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;QACxC,IAAI,QAAQ,KAAK,WAAW,EAAE;
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{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":";;;;;AAAA,kCAAqC;AAErC,oDAA4C;AAW5C,MAAqB,kBAAmB,SAAQ,eAG/C;IAGC,YACE,UAAiD,EACjD,QAAqB,EACrB,gBAAkC;QAElC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;QACxC,IAAI,QAAQ,KAAK,WAAW,EAAE,CAAC;YAC7B,MAAM,IAAI,SAAS,CACjB,8CAA8C,QAAQ,EAAE,CACzD,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,MAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CACpC,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QAED,MAAM,SAAS,GAAG,IAAI,CAAC,aAAa,EAAE,CAAA;QACtC,MAAM,IAAI,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;QACxC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,MAAM,CACxB,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QACH,CAAC;QAED,OAAO,IAAI,CAAA;IACb,CAAC;IAED,UAAU;IACV,eAAe;QACb,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,eAAe,CAAA;QACtD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,KAAK,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,aAAa;QACX,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,cAAc,CAAA;QACrD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;CACF;AA3DD,qCA2DC;AAED,+BAA+B;KAC5B,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,IAAA,kBAAW,EAAC,kBAAkB,EAAE,MAAM,CAAC,CAAC,CAAA"}
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{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.ts"],"names":[],"mappings":";;;;;AAAA,yCAAiD;AAEjD,oDAAoD;AAIpD,uCAAkD;AAElD,MAAqB,kBAAmB,SAAQ,eAG/C;IACC,YACE,UAAmD,EACnD,QAAqB;QAErB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,QAAQ,KAAK,WAAW,EAAE;
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{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.ts"],"names":[],"mappings":";;;;;AAAA,yCAAiD;AAEjD,oDAAoD;AAIpD,uCAAkD;AAElD,MAAqB,kBAAmB,SAAQ,eAG/C;IACC,YACE,UAAmD,EACnD,QAAqB;QAErB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,QAAQ,KAAK,WAAW,EAAE,CAAC;YAC7B,MAAM,IAAI,SAAS,CACjB,kDAAkD,QAAQ,EAAE,CAC7D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,EAAE,CACnD,CAAA;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,gBAAgB,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IACpD,CAAC;IAED,gBAAgB,CAAC,YAA2B,EAAE,MAAc;QAC1D,MAAM,UAAU,GAAG,YAAY,CAAC,OAAO,CAAA;QACvC,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,6BAA6B;QAC7B,MAAM,aAAa,GAAG,MAAM,CAAC,YAAY,CAAA;QACzC,IAAI,YAAY,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,OACE,UAAU,CAAC,YAAY,CAAC,KAAK,QAAQ;YACrC,YAAY,GAAG,UAAU,CAAC,MAAM,EAChC,CAAC;YACD,IAAI,YAAY,KAAK,UAAU,CAAC,MAAM,EAAE,CAAC;gBACvC,MAAM,IAAI,gCAAsB,CAC9B,qDAAqD,CACtD,CAAA;YACH,CAAC;YACD,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACjC,CAAC;QACD,MAAM,CAAC,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACtC,OAAO,UAAU,CAAC,QAAQ,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;IACzD,CAAC;CACF;AArDD,qCAqDC"}
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{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,yCAAyE;AACzE,oDAAoD;AACpD,kCAAmC;AAGnC,uCAAkD;AAGlD,MAAqB,aAAc,SAAQ,eAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;
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{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,yCAAyE;AACzE,oDAAoD;AACpD,kCAAmC;AAGnC,uCAAkD;AAGlD,MAAqB,aAAc,SAAQ,eAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,EAAE,CACnD,CAAA;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC/C,CAAC;IAED,UAAU,CAAC,YAA2B,EAAE,MAAc;QACpD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAS,EACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;QACD,MAAM,CAAC,YAAY,GAAG,MAAM,CAAC,YAAY,GAAG,SAAS,CAAA;QACrD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,WAAW,CAAC,YAA2B,EAAE,MAAc;QACrD,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YACvD,MAAM,IAAI,gCAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC,CAAA;IACpD,CAAC;CACF;AA3DD,gCA2DC"}
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{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,UAAW,SAAQ,eAGvC;IACC,YAAY,UAAuC,EAAE,QAAe;QAClE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;
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{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,UAAW,SAAQ,eAGvC;IACC,YAAY,UAAuC,EAAE,QAAe;QAClE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,8CAA8C,CAC/D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,MAAM,GAAG,CAAC,CAAA;QAEd,OAAO,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YAClE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;QACrB,CAAC;QAED,MAAM,QAAQ,GAAG,IAAA,iBAAO,EACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,MAAM,GAAG,CAAC,CACX,CAAA;QAED,MAAM,KAAK,GAAG,QAAQ,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QAC5C,OAAO,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACvC,CAAC;CACF;AAlCD,6BAkCC"}
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{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":";;;AAAA,MAAa,sBAAuB,SAAQ,KAAK;CAAG;AAApD,wDAAoD;AAEpD,SAAgB,OAAO,CACrB,IAAY,EACZ,MAAqD,EACrD,OAAe;IAEf,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IACE,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC;QAC5D,IAAI,CAAC,MAAM,EACX;
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{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":";;;AAAA,MAAa,sBAAuB,SAAQ,KAAK;CAAG;AAApD,wDAAoD;AAEpD,SAAgB,OAAO,CACrB,IAAY,EACZ,MAAqD,EACrD,OAAe;IAEf,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IACE,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC;QAC5D,IAAI,CAAC,MAAM,EACX,CAAC;QACD,MAAM,IAAI,sBAAsB,CAC9B,6DAA6D,CAC9D,CAAA;IACH,CAAC;IACD,KAAK,IAAI,IAAI,GAAG,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC;QACtC,yDAAyD;QACzD,GAAG,KAAK,CAAC,CAAA;QACT,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QAC5D,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;QACvB,IAAI,MAAM,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC;YAC3B,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;QAC1B,CAAC;QACD,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAzBD,0BAyBC"}
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{"version":3,"file":"huffman.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/huffman.ts"],"names":[],"mappings":";;;;;AAAA,yCAAiD;AACjD,oDAAoD;AACpD,uCAAmC;AAMnC,SAAS,eAAe,CAAC,EAAU;IACjC,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,GAAG,UAAU,CAAA;IACrC,CAAC,GAAG,CAAC,CAAC,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,UAAU,CAAC,CAAA;IAC9C,OAAO,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,UAAU,CAAC,GAAG,UAAU,CAAC,IAAI,EAAE,CAAA;AAC3D,CAAC;AAID,MAAqB,eAAgB,SAAQ,eAG5C;IAUC,YACE,UAAyC,EACzC,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAbrB,UAAK,GAAyB,EAAE,CAAA;QAChC,aAAQ,GAA6B,EAAE,CAAA;QACvC,kBAAa,GAAW,EAAE,CAAA;QAC1B,gBAAW,GAAW,EAAE,CAAA;QACxB,0BAAqB,GAAa,EAAE,CAAA;QACpC,mBAAc,GAAa,EAAE,CAAA;QAC7B,8BAAyB,GAAa,EAAE,CAAA;QACxC,mBAAc,GAAa,EAAE,CAAA;QAOnC,IAAI,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE;
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+
{"version":3,"file":"compressionScheme.js","sourceRoot":"","sources":["../../../src/cramFile/container/compressionScheme.ts"],"names":[],"mappings":";;AAAA,sCAA4C;AAI5C,yCAAiD;AAMjD,sDAAsD;AACtD,aAAa;AACb,MAAM,eAAe,GAAG;IACtB,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,gBAAgB;IAChB,gBAAgB;CACR,CAAA;AAIV,SAAS,uBAAuB,CAAC,SAAmB;IAClD,MAAM,MAAM,GAAe,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IACvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IAC1B,CAAC;IAED,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,OAAO,MAAM,CAAA;AACf,CAAC;AAMD,MAAqB,8BAA8B;IAcjD,YAAY,OAA8B;QARnC,yBAAoB,GAAoB,EAAE,CAAA;QAC1C,kBAAa,GAA8B,EAAE,CAAA;QAC7C,gBAAW,GAAiC,EAAE,CAAA;QAOnD,+BAA+B;QAC/B,iEAAiE;QACjE,IAAI,CAAC,iBAAiB,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAChD,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QACtC,IAAI,CAAC,iBAAiB,GAAG,CAAC,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAClD,IAAI,CAAC,gBAAgB,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAC/C,IAAI,CAAC,kBAAkB,GAAG,uBAAuB,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAC,CAAA;QAC1E,IAAI,CAAC,kBAAkB,GAAG,OAAO,CAAC,kBAAkB,CAAA;QACpD,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,WAAW,CAAA;QACtC,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,YAAY,CAAA;QACxC,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,CAAA;QAC1B,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,YAAY,CAAA;IAC1C,CAAC;IAED;;;OAGG;IACH,cAAc,CAAC,OAAe;QAC5B,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EAAE,CAAC;YACjC,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC9C,IAAI,YAAY,EAAE,CAAC;gBACjB,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,IAAA,yBAAgB,EAC5C,YAAY,EACZ,WAAW,CACZ,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;IACpC,CAAC;IAED;;;;OAIG;IACH,WAAW,CAAC,SAAiB;QAC3B,OAAO,IAAI,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAA;IACzC,CAAC;IAED,qBAAqB,CACnB,cAA2B;QAE3B,IAAI,CAAC,GACH,IAAI,CAAC,oBAAoB,CAAC,cAAc,CAAC,CAAA;QAC3C,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YACpB,MAAM,YAAY,GAAG,IAAI,CAAC,kBAAkB,CAAC,cAAc,CAAC,CAAA;YAC5D,IAAI,YAAY,EAAE,CAAC;gBACjB,MAAM,QAAQ,GAAG,eAAe,CAAC,cAAc,CAAC,CAAA;gBAChD,IAAI,CAAC,QAAQ,EAAE,CAAC;oBACd,MAAM,IAAI,2BAAkB,CAC1B,oBAAoB,cAAc,yCAAyC,CAC5E,CAAA;gBACH,CAAC;gBACD,CAAC,GAAG,IAAA,yBAAgB,EAAC,YAAY,EAAE,QAAQ,CAAC,CAAA;gBAC5C,+CAA+C;gBAC/C,IAAI,CAAC,oBAAoB,CAAC,cAAc,CAAC,GAAG,CAAmB,CAAA;YACjE,CAAC;QACH,CAAC;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,MAAM,IAAI,GAAQ,EAAE,CAAA;QACpB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAC5B,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;gBACrB,OAAM;YACR,CAAC;YACD,IAAI,CAAC,CAAC,CAAC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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,yCAAiD;AAEjD,kCAA0D;AAC1D,qDAAgC;AAChC,4EAAgE;AAGhE,MAAqB,aAAa;IAChC,YACS,IAAc,EACd,YAAoB;QADpB,SAAI,GAAJ,IAAI,CAAU;QACd,iBAAY,GAAZ,YAAY,CAAQ;IAC1B,CAAC;IAEJ,UAAU;IACV,SAAS;QACP,OAAO,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACJ,yBAAyB;;YAC7B,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAE9C,gFAAgF;YAChF,IAAI,CAAC,eAAe,CAAC,UAAU,EAAE;
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,yCAAiD;AAEjD,kCAA0D;AAC1D,qDAAgC;AAChC,4EAAgE;AAGhE,MAAqB,aAAa;IAChC,YACS,IAAc,EACd,YAAoB;QADpB,SAAI,GAAJ,IAAI,CAAU;QACd,iBAAY,GAAZ,YAAY,CAAQ;IAC1B,CAAC;IAEJ,UAAU;IACV,SAAS;QACP,OAAO,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACJ,yBAAyB;;YAC7B,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAE9C,gFAAgF;YAChF,IAAI,CAAC,eAAe,CAAC,UAAU,EAAE,CAAC;gBAChC,OAAO,IAAI,CAAA;YACb,CAAC;YACD,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,iBAAiB,EAAE,CAAA;YAC1D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;YACxC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,IAAI,KAAK,CAAC,WAAW,KAAK,oBAAoB,EAAE,CAAC;gBAC/C,MAAM,IAAI,2BAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,yDAAyD,CACnG,CAAA;YACH,CAAC;YACD,MAAM,OAAO,GAAG,IAAA,gBAAS,EACvB,KAAK,CAAC,OAAO,EACb,cAAc,CAAC,qBAAqB,CAAC,MAAM,EAC3C,CAAC,EACD,KAAK,CAAC,eAAe,CACtB,CAAA;YACD,uCACK,KAAK,KACR,aAAa,EAAE,OAAO,IACvB;QACH,CAAC;KAAA;IAEK,aAAa;;YACjB,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;QAC1D,CAAC;KAAA;IAED,kFAAkF;IAClF,UAAU;IACJ,oBAAoB;;YACxB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,yBAAyB,EAAE,CAAA;YACrD,IAAI,CAAC,MAAM,EAAE,CAAC;gBACZ,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,OAAO,IAAI,2BAA8B,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;QACjE,CAAC;KAAA;IAED,QAAQ,CAAC,aAAqB,EAAE,SAAiB;QAC/C,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,IAAI,eAAS,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,CAAA;IACtD,CAAC;IAEK,oBAAoB,CAAC,QAAgB;;YACzC,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,iBAAiB,EAAE,CAAA;YAC1D,MAAM,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;YACrE,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;YAEjD,IAAI,QAAQ,IAAI,QAAQ,EAAE,CAAC;gBACzB,OAAO,SAAS,CAAA;YAClB,CAAC;YAED,wEAAwE;YACxE,iDAAiD;YACjD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,oBAAoB,CAAC,SAAS,CAAC,CAAA;YACjE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,oBAAoB,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;YACzE,MAAM,OAAO,GAAG,IAAA,gBAAS,EAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAQ,CAAA;YACrE,MAAM,gBAAgB,GAAG,IAAA,eAAQ,EAAC,OAAO,CAAC,YAAY,CAAC,CAAA;YACvD,IAAI,QAAQ,GAAG,OAAO,CAAC,MAAM,IAAI,QAAQ,EAAE,CAAC;gBAC1C,OAAO,CAAC,IAAI,CACV,GAAG,IAAI,CAAC,IAAI,yBAAyB,QAAQ,4CAA4C,OAAO,CAAC,MAAM,yEAAyE,CACjL,CAAA;gBACD,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAC/B,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,CACrD,CAAA;YACD,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAClB,MAAM,EACN,CAAC,EACD,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,EACpD,QAAQ,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,CAC5C,CAAA;YACD,MAAM,OAAO,GAAG,IAAA,gBAAS,EAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;YAE9D,IAAI,IAAI,CAAC,IAAI,CAAC,iBAAiB,IAAI,OAAO,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;gBAC/D,MAAM,IAAI,CAAC,IAAI,CAAC,UAAU,CACxB,QAAQ,EACR,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,CAAC,EACpD,OAAO,CAAC,KAAK,EACb,0CAA0C,QAAQ,EAAE,CACrD,CAAA;YACH,CAAC;YAED,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,EAAE;gBACrD,KAAK,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB;gBACvD,YAAY,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,QAAQ;aAC1E,CAAC,CAAA;YAEF,OAAO,cAAc,CAAA;QACvB,CAAC;KAAA;CACF;AA9GD,gCA8GC;AAED,0DAA0D;KACvD,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,IAAA,kBAAW,EAAC,aAAa,EAAE,MAAM,CAAC,CAAC,CAAA"}
|
package/dist/cramFile/file.d.ts
CHANGED
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
/// <reference path="../../src/typings/binary-parser.d.ts" />
|
|
1
2
|
/// <reference types="node" />
|
|
2
3
|
import QuickLRU from 'quick-lru';
|
|
3
4
|
import { Parser } from '@gmod/binary-parser';
|
|
@@ -40,7 +41,13 @@ export default class CramFile {
|
|
|
40
41
|
}>;
|
|
41
42
|
stat(): Promise<import("generic-filehandle").Stats>;
|
|
42
43
|
getDefinition(): Promise<any>;
|
|
43
|
-
getSamHeader(): Promise<
|
|
44
|
+
getSamHeader(): Promise<{
|
|
45
|
+
tag: string;
|
|
46
|
+
data: {
|
|
47
|
+
tag: string;
|
|
48
|
+
value: string | undefined;
|
|
49
|
+
}[];
|
|
50
|
+
}[]>;
|
|
44
51
|
getHeaderText(): Promise<string | undefined>;
|
|
45
52
|
getSectionParsers(): Promise<{
|
|
46
53
|
cramFileDefinition: {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
{"version":3,"file":"record.js","sourceRoot":"","sources":["../../src/cramFile/record.ts"],"names":[],"mappings":";;;;;;AAAA,4DAAmC;AAoBnC,SAAS,kBAAkB,CACzB,UAAsB,EACtB,SAAoB;IAEpB,0CAA0C;IAC1C,IAAI,CAAC,UAAU,CAAC,WAAW,IAAI,CAAC,UAAU,CAAC,UAAU,EAAE,CAAC;QACtD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,IAAI,UAAU,CAAC,cAAc,EAAE,EAAE,CAAC;QAChC,OAAO,IAAI,CAAA;IACb,CAAC;IAED,+CAA+C;IAC/C,MAAM,eAAe,GAAG,UAAU,CAAC,cAAc,GAAG,SAAS,CAAC,KAAK,CAAA;IAEnE,IAAI,CAAC,UAAU,CAAC,YAAY,EAAE,CAAC;QAC7B,OAAO,SAAS,CAAC,GAAG;aACjB,MAAM,CAAC,eAAe,EAAE,UAAU,CAAC,WAAW,CAAC;aAC/C,WAAW,EAAE,CAAA;IAClB,CAAC;IAED,IAAI,KAAK,GAAG,EAAE,CAAA;IACd,IAAI,SAAS,GAAG,eAAe,CAAA;IAC/B,IAAI,kBAAkB,GAAG,CAAC,CAAA;IAC1B,OAAO,KAAK,CAAC,MAAM,GAAG,UAAU,CAAC,UAAU,EAAE,CAAC;QAC5C,IAAI,kBAAkB,GAAG,UAAU,CAAC,YAAY,CAAC,MAAM,EAAE,CAAC;YACxD,MAAM,OAAO,GAAG,UAAU,CAAC,YAAY,CAAC,kBAAkB,CAAC,CAAA;YAC3D,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;gBACjD,kBAAkB,IAAI,CAAC,CAAA;YACzB,CAAC;iBAAM,IAAI,OAAO,CAAC,GAAG,KAAK,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAC5C,2BAA2B;gBAC3B,kBAAkB,IAAI,CAAC,CAAA;gBAEvB,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBACzB,sCAAsC;oBACtC,MAAM,KAAK,GAAG,OAAO,CAAC,IAAI,CAAA;oBAC1B,KAAK,IAAI,KAAK,CAAA;oBACd,SAAS,IAAI,KAAK,CAAC,MAAM,CAAA;gBAC3B,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,mCAAmC;oBACnC,0DAA0D;oBAC1D,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;oBACxB,SAAS,IAAI,CAAC,CAAA;gBAChB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,oBAAoB;oBACpB,KAAK,IAAI,OAAO,CAAC,GAAG,CAAA;oBACpB,SAAS,IAAI,CAAC,CAAA;gBAChB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,YAAY;oBACZ,KAAK,IAAI,OAAO,CAAC,IAAI,CAAA;gBACvB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,WAAW;oBACX,SAAS,IAAI,OAAO,CAAC,IAAI,CAAA;gBAC3B,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,qBAAqB;oBACrB,KAAK,IAAI,OAAO,CAAC,IAAI,CAAA;gBACvB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,oCAAoC;oBACpC,aAAa;oBACb,iDAAiD;oBACjD,SAAS,IAAI,OAAO,CAAC,IAAI,CAAA;gBAC3B,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,4DAA4D;oBAC5D,iEAAiE;oBACjE,KAAK,IAAI,OAAO,CAAC,IAAI,CAAA;gBACvB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,sBAAsB;gBACxB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,wBAAwB;gBAC1B,CAAC;YACH,CAAC;iBAAM,IAAI,kBAAkB,GAAG,UAAU,CAAC,YAAY,CAAC,MAAM,EAAE,CAAC;gBAC/D,2DAA2D;gBAC3D,MAAM,KAAK,GAAG,SAAS,CAAC,GAAG,CAAC,MAAM,CAChC,SAAS,EACT,UAAU,CAAC,YAAY,CAAC,kBAAkB,CAAC,CAAC,GAAG,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,CACnE,CAAA;gBACD,KAAK,IAAI,KAAK,CAAA;gBACd,SAAS,IAAI,KAAK,CAAC,MAAM,CAAA;YAC3B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,2DAA2D;YAC3D,MAAM,KAAK,GAAG,SAAS,CAAC,GAAG,CAAC,MAAM,CAChC,SAAS,EACT,UAAU,CAAC,UAAU,GAAG,KAAK,CAAC,MAAM,CACrC,CAAA;YACD,KAAK,IAAI,KAAK,CAAA;YACd,SAAS,IAAI,KAAK,CAAC,MAAM,CAAA;QAC3B,CAAC;IACH,CAAC;IAED,OAAO,KAAK,CAAC,WAAW,EAAE,CAAA;AAC5B,CAAC;AAED,MAAM,WAAW,GAAG;IAClB,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;CACL,CAAA;AAED,SAAS,sBAAsB,CAC7B,UAAsB,EACtB,SAAoB,EACpB,iBAAiD,EACjD,WAAwB;IAExB,IAAI,CAAC,SAAS,EAAE,CAAC;QACf,OAAM;IACR,CAAC;IAED,8DAA8D;IAC9D,MAAM,QAAQ,GAAG,WAAW,CAAC,MAAM,GAAG,SAAS,CAAC,KAAK,CAAA;IACrD,MAAM,OAAO,GAAG,SAAS,CAAC,GAAG,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;IAC9C,IAAI,OAAO,EAAE,CAAC;QACZ,WAAW,CAAC,GAAG,GAAG,OAAO,CAAA;IAC3B,CAAC;IACD,IAAI,UAAU,GAAI,WAAmB,CAAC,OAAO,CAAC,CAAA;IAC9C,IAAI,UAAU,KAAK,SAAS,EAAE,CAAC;QAC7B,UAAU,GAAG,CAAC,CAAA;IAChB,CAAC;IACD,MAAM,kBAAkB,GAAG,iBAAiB,CAAC,kBAAkB,CAAC,UAAU,CAAC,CAAA;IAC3E,MAAM,IAAI,GAAG,kBAAkB,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACjD,IAAI,IAAI,EAAE,CAAC;QACT,WAAW,CAAC,GAAG,GAAG,IAAI,CAAA;IACxB,CAAC;AACH,CAAC;AAWY,QAAA,QAAQ,GAAG;IACtB,CAAC,GAAG,EAAE,QAAQ,CAAC;IACf,CAAC,GAAG,EAAE,gBAAgB,CAAC;IACvB,CAAC,GAAG,EAAE,iBAAiB,CAAC;IACxB,CAAC,GAAG,EAAE,cAAc,CAAC;IACrB,CAAC,IAAI,EAAE,qBAAqB,CAAC;IAC7B,4CAA4C;IAC5C,CAAC,IAAI,EAAE,yBAAyB,CAAC;IACjC,iBAAiB;IACjB,CAAC,IAAI,EAAE,OAAO,CAAC;IACf,iBAAiB;IACjB,CAAC,IAAI,EAAE,OAAO,CAAC;IACf,yBAAyB;IACzB,CAAC,KAAK,EAAE,WAAW,CAAC;IACpB,cAAc;IACd,CAAC,KAAK,EAAE,UAAU,CAAC;IACnB,4BAA4B;IAC5B,CAAC,KAAK,EAAE,WAAW,CAAC;IACpB,2BAA2B;IAC3B,CAAC,KAAK,EAAE,eAAe,CAAC;CAChB,CAAA;AAEG,QAAA,SAAS,GAAG;IACvB,CAAC,GAAG,EAAE,yBAAyB,CAAC;IAChC,CAAC,GAAG,EAAE,UAAU,CAAC;IACjB,CAAC,GAAG,EAAE,oBAAoB,CAAC;IAC3B,CAAC,GAAG,EAAE,sBAAsB,CAAC;CACrB,CAAA;AAEG,QAAA,SAAS,GAAG;IACvB,CAAC,GAAG,EAAE,kBAAkB,CAAC;IACzB,CAAC,GAAG,EAAE,UAAU,CAAC;CACT,CAAA;AAcV,SAAS,eAAe,CACtB,CAAsC;IAEtC,MAAM,CAAC,GAAQ,EAAE,CAAA;IACjB,KAAK,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QAC7B,CAAC,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,KAAa,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,CAAA;QACpD,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,KAAa,EAAE,EAAE,CAAC,KAAK,GAAG,IAAI,CAAA;IACnD,CAAC;IAED,OAAO,CAAC,CAAA;AACV,CAAC;AAEY,QAAA,eAAe,GAAG,eAAe,CAAC,gBAAQ,CAAC,CAAA;AAC3C,QAAA,gBAAgB,GAAG,eAAe,CAAC,iBAAS,CAAC,CAAA;AAC7C,QAAA,gBAAgB,GAAG,eAAe,CAAC,iBAAS,CAAC,CAAA;AAE1D;;GAEG;AACH,MAAqB,UAAU;IAqB7B,YAAY,E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|
@@ -39,7 +39,7 @@ const cramBlockHeader = {
|
|
|
39
39
|
'FILE_HEADER',
|
|
40
40
|
'COMPRESSION_HEADER',
|
|
41
41
|
'MAPPED_SLICE_HEADER',
|
|
42
|
-
'UNMAPPED_SLICE_HEADER',
|
|
42
|
+
'UNMAPPED_SLICE_HEADER', // < only used in cram v1
|
|
43
43
|
'EXTERNAL_DATA',
|
|
44
44
|
'CORE_DATA',
|
|
45
45
|
][b];
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|
@@ -214,9 +214,9 @@ const versionedParsers = {
|
|
|
214
214
|
.choice('parameters', {
|
|
215
215
|
tag: 'codecId',
|
|
216
216
|
choices: {
|
|
217
|
-
0: new binary_parser_1.Parser(),
|
|
218
|
-
1: new binary_parser_1.Parser().itf8('blockContentId'),
|
|
219
|
-
2: new binary_parser_1.Parser().itf8('offset').itf8('M'),
|
|
217
|
+
0: new binary_parser_1.Parser(), // NULL
|
|
218
|
+
1: new binary_parser_1.Parser().itf8('blockContentId'), // EXTERNAL
|
|
219
|
+
2: new binary_parser_1.Parser().itf8('offset').itf8('M'), // GOLOMB,
|
|
220
220
|
// HUFFMAN_INT
|
|
221
221
|
3: binary_parser_1.Parser.start()
|
|
222
222
|
.itf8('numCodes')
|
|
@@ -228,9 +228,9 @@ const versionedParsers = {
|
|
|
228
228
|
.nest('valuesEncoding', { type: 'cramEncoding' }),
|
|
229
229
|
// BYTE_ARRAY_STOP is a little different for CRAM v1
|
|
230
230
|
5: new binary_parser_1.Parser().uint8('stopByte').itf8('blockContentId'),
|
|
231
|
-
6: new binary_parser_1.Parser().itf8('offset').itf8('length'),
|
|
232
|
-
7: new binary_parser_1.Parser().itf8('offset').itf8('K'),
|
|
233
|
-
8: new binary_parser_1.Parser().itf8('offset').itf8('log2m'),
|
|
231
|
+
6: new binary_parser_1.Parser().itf8('offset').itf8('length'), // BETA
|
|
232
|
+
7: new binary_parser_1.Parser().itf8('offset').itf8('K'), // SUBEXP
|
|
233
|
+
8: new binary_parser_1.Parser().itf8('offset').itf8('log2m'), // GOLOMB_RICE
|
|
234
234
|
9: new binary_parser_1.Parser().itf8('offset'), // GAMMA
|
|
235
235
|
},
|
|
236
236
|
});
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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@@ -140,7 +140,7 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
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140
140
|
// map of operator name -> data series name
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|
141
141
|
const data1Schema = {
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|
142
142
|
B: ['character', 'BA'],
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|
143
|
-
S: ['string', majorVersion > 1 ? 'SC' : 'IN'],
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143
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+
S: ['string', majorVersion > 1 ? 'SC' : 'IN'], // IN if cram v1, SC otherwise
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|
144
144
|
X: ['number', 'BS'],
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|
145
145
|
D: ['number', 'DL'],
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|
146
146
|
I: ['string', 'IN'],
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@@ -1 +1 @@
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|
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1
|
-
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1
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1
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+
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package/dist/cramFile/util.d.ts
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/cramFile/util.ts"],"names":[],"mappings":";;;;;;AAAA,8CAAqB;AAErB,8CAAyD;AAEzD,SAAgB,QAAQ,CAAC,CAAS;IAChC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;
|
|
1
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package/dist/io/index.js.map
CHANGED
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