@gmod/cram 3.0.7 → 4.0.0
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 +70 -87
- package/dist/craiIndex.js.map +1 -1
- package/dist/cram-bundle.js +1 -1
- package/dist/cramFile/codecs/_base.d.ts +1 -1
- package/dist/cramFile/codecs/beta.d.ts +2 -2
- package/dist/cramFile/codecs/beta.js +1 -1
- package/dist/cramFile/codecs/beta.js.map +1 -1
- package/dist/cramFile/codecs/byteArrayLength.d.ts +2 -2
- package/dist/cramFile/codecs/byteArrayStop.d.ts +4 -4
- package/dist/cramFile/codecs/byteArrayStop.js +1 -1
- package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
- package/dist/cramFile/codecs/external.d.ts +1 -1
- package/dist/cramFile/codecs/external.js +1 -1
- package/dist/cramFile/codecs/external.js.map +1 -1
- package/dist/cramFile/codecs/gamma.d.ts +1 -1
- package/dist/cramFile/codecs/gamma.js +1 -1
- package/dist/cramFile/codecs/gamma.js.map +1 -1
- package/dist/cramFile/codecs/getBits.d.ts +1 -1
- package/dist/cramFile/codecs/getBits.js.map +1 -1
- package/dist/cramFile/codecs/huffman.d.ts +1 -1
- package/dist/cramFile/codecs/huffman.js +1 -1
- package/dist/cramFile/codecs/huffman.js.map +1 -1
- package/dist/cramFile/codecs/index.d.ts +1 -1
- package/dist/cramFile/codecs/index.js +5 -5
- package/dist/cramFile/codecs/index.js.map +1 -1
- package/dist/cramFile/codecs/subexp.d.ts +2 -2
- package/dist/cramFile/codecs/subexp.js +1 -1
- package/dist/cramFile/codecs/subexp.js.map +1 -1
- package/dist/cramFile/container/compressionScheme.d.ts +2 -2
- package/dist/cramFile/container/compressionScheme.js +1 -1
- package/dist/cramFile/container/compressionScheme.js.map +1 -1
- package/dist/cramFile/container/index.d.ts +1 -2
- package/dist/cramFile/container/index.js +62 -79
- package/dist/cramFile/container/index.js.map +1 -1
- package/dist/cramFile/file.d.ts +9 -13
- package/dist/cramFile/file.js +218 -247
- package/dist/cramFile/file.js.map +1 -1
- package/dist/cramFile/record.js +2 -2
- package/dist/cramFile/record.js.map +1 -1
- package/dist/cramFile/sectionParsers.d.ts +16 -16
- package/dist/cramFile/sectionParsers.js +12 -9
- package/dist/cramFile/sectionParsers.js.map +1 -1
- package/dist/cramFile/slice/decodeRecord.d.ts +3 -3
- package/dist/cramFile/slice/decodeRecord.js +11 -11
- package/dist/cramFile/slice/decodeRecord.js.map +1 -1
- package/dist/cramFile/slice/index.d.ts +2 -2
- package/dist/cramFile/slice/index.js +241 -262
- package/dist/cramFile/slice/index.js.map +1 -1
- package/dist/cramFile/util.d.ts +4 -2
- package/dist/cramFile/util.js +29 -6
- package/dist/cramFile/util.js.map +1 -1
- package/dist/htscodecs/arith_gen.d.ts +9 -17
- package/dist/htscodecs/arith_gen.js +32 -272
- package/dist/htscodecs/arith_gen.js.map +1 -1
- package/dist/htscodecs/fqzcomp.d.ts +1 -2
- package/dist/htscodecs/fqzcomp.js +2 -421
- package/dist/htscodecs/fqzcomp.js.map +1 -1
- package/dist/htscodecs/index.d.ts +5 -5
- package/dist/htscodecs/index.js +10 -10
- package/dist/htscodecs/index.js.map +1 -1
- package/dist/htscodecs/iostream.d.ts +2 -1
- package/dist/htscodecs/iostream.js +3 -2
- package/dist/htscodecs/iostream.js.map +1 -1
- package/dist/htscodecs/rans.d.ts +1 -2
- package/dist/htscodecs/rans.js +3 -270
- package/dist/htscodecs/rans.js.map +1 -1
- package/dist/htscodecs/rans4x16.d.ts +0 -1
- package/dist/htscodecs/rans4x16.js +6 -497
- package/dist/htscodecs/rans4x16.js.map +1 -1
- package/dist/htscodecs/tok3.js +17 -1
- package/dist/htscodecs/tok3.js.map +1 -1
- package/dist/index.d.ts +1 -1
- package/dist/index.js +2 -2
- package/dist/index.js.map +1 -1
- package/dist/indexedCramFile.d.ts +4 -4
- package/dist/indexedCramFile.js +97 -108
- package/dist/indexedCramFile.js.map +1 -1
- package/dist/io/index.d.ts +2 -2
- package/dist/io/index.js +6 -6
- package/dist/io/index.js.map +1 -1
- package/dist/rans/constants.d.ts +1 -1
- package/dist/rans/constants.js +1 -1
- package/dist/rans/constants.js.map +1 -1
- package/dist/rans/d04.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 +5 -5
- package/dist/rans/index.js.map +1 -1
- package/dist/unzip.d.ts +1 -1
- package/dist/unzip.js +5 -3
- package/dist/unzip.js.map +1 -1
- package/esm/craiIndex.js +10 -12
- package/esm/craiIndex.js.map +1 -1
- package/esm/cramFile/codecs/_base.d.ts +1 -1
- package/esm/cramFile/codecs/beta.d.ts +2 -2
- package/esm/cramFile/codecs/beta.js +1 -1
- package/esm/cramFile/codecs/beta.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayLength.d.ts +2 -2
- package/esm/cramFile/codecs/byteArrayStop.d.ts +4 -4
- package/esm/cramFile/codecs/byteArrayStop.js +1 -1
- package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
- package/esm/cramFile/codecs/external.d.ts +1 -1
- package/esm/cramFile/codecs/external.js +1 -1
- package/esm/cramFile/codecs/external.js.map +1 -1
- package/esm/cramFile/codecs/gamma.d.ts +1 -1
- package/esm/cramFile/codecs/gamma.js +1 -1
- package/esm/cramFile/codecs/gamma.js.map +1 -1
- package/esm/cramFile/codecs/getBits.d.ts +1 -1
- package/esm/cramFile/codecs/getBits.js.map +1 -1
- package/esm/cramFile/codecs/huffman.d.ts +1 -1
- package/esm/cramFile/codecs/huffman.js +1 -1
- package/esm/cramFile/codecs/huffman.js.map +1 -1
- package/esm/cramFile/codecs/index.d.ts +1 -1
- package/esm/cramFile/codecs/index.js +5 -5
- package/esm/cramFile/codecs/index.js.map +1 -1
- package/esm/cramFile/codecs/subexp.d.ts +2 -2
- package/esm/cramFile/codecs/subexp.js +1 -1
- package/esm/cramFile/codecs/subexp.js.map +1 -1
- package/esm/cramFile/container/compressionScheme.d.ts +2 -2
- package/esm/cramFile/container/compressionScheme.js +1 -1
- package/esm/cramFile/container/compressionScheme.js.map +1 -1
- package/esm/cramFile/container/index.d.ts +1 -2
- package/esm/cramFile/container/index.js +4 -7
- package/esm/cramFile/container/index.js.map +1 -1
- package/esm/cramFile/file.d.ts +9 -13
- package/esm/cramFile/file.js +47 -52
- package/esm/cramFile/file.js.map +1 -1
- package/esm/cramFile/record.js +2 -2
- package/esm/cramFile/record.js.map +1 -1
- package/esm/cramFile/sectionParsers.d.ts +16 -16
- package/esm/cramFile/sectionParsers.js +7 -7
- package/esm/cramFile/sectionParsers.js.map +1 -1
- package/esm/cramFile/slice/decodeRecord.d.ts +3 -3
- package/esm/cramFile/slice/decodeRecord.js +11 -11
- package/esm/cramFile/slice/decodeRecord.js.map +1 -1
- package/esm/cramFile/slice/index.d.ts +2 -2
- package/esm/cramFile/slice/index.js +7 -6
- package/esm/cramFile/slice/index.js.map +1 -1
- package/esm/cramFile/util.d.ts +4 -2
- package/esm/cramFile/util.js +19 -2
- package/esm/cramFile/util.js.map +1 -1
- package/esm/htscodecs/arith_gen.d.ts +9 -17
- package/esm/htscodecs/arith_gen.js +32 -272
- package/esm/htscodecs/arith_gen.js.map +1 -1
- package/esm/htscodecs/fqzcomp.d.ts +1 -2
- package/esm/htscodecs/fqzcomp.js +2 -421
- package/esm/htscodecs/fqzcomp.js.map +1 -1
- package/esm/htscodecs/index.d.ts +5 -5
- package/esm/htscodecs/index.js +10 -10
- package/esm/htscodecs/index.js.map +1 -1
- package/esm/htscodecs/iostream.d.ts +2 -1
- package/esm/htscodecs/iostream.js +3 -2
- package/esm/htscodecs/iostream.js.map +1 -1
- package/esm/htscodecs/rans.d.ts +1 -2
- package/esm/htscodecs/rans.js +3 -270
- package/esm/htscodecs/rans.js.map +1 -1
- package/esm/htscodecs/rans4x16.d.ts +0 -1
- package/esm/htscodecs/rans4x16.js +6 -497
- package/esm/htscodecs/rans4x16.js.map +1 -1
- package/esm/htscodecs/tok3.js +17 -1
- package/esm/htscodecs/tok3.js.map +1 -1
- package/esm/index.d.ts +1 -1
- package/esm/index.js +1 -1
- package/esm/index.js.map +1 -1
- package/esm/indexedCramFile.d.ts +4 -4
- package/esm/indexedCramFile.js +10 -10
- package/esm/indexedCramFile.js.map +1 -1
- package/esm/io/index.d.ts +2 -2
- package/esm/io/index.js +1 -1
- package/esm/io/index.js.map +1 -1
- package/esm/rans/constants.d.ts +1 -1
- package/esm/rans/constants.js +1 -1
- package/esm/rans/constants.js.map +1 -1
- package/esm/rans/d04.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 +5 -5
- package/esm/rans/index.js.map +1 -1
- package/esm/unzip.d.ts +1 -1
- package/esm/unzip.js +4 -1
- package/esm/unzip.js.map +1 -1
- package/package.json +7 -9
- package/src/craiIndex.ts +17 -16
- package/src/cramFile/codecs/_base.ts +1 -1
- package/src/cramFile/codecs/beta.ts +3 -3
- package/src/cramFile/codecs/byteArrayLength.ts +1 -1
- package/src/cramFile/codecs/byteArrayStop.ts +3 -4
- package/src/cramFile/codecs/external.ts +3 -3
- package/src/cramFile/codecs/gamma.ts +2 -2
- package/src/cramFile/codecs/getBits.ts +1 -1
- package/src/cramFile/codecs/huffman.ts +2 -3
- package/src/cramFile/codecs/index.ts +7 -8
- package/src/cramFile/codecs/subexp.ts +3 -3
- package/src/cramFile/container/compressionScheme.ts +3 -3
- package/src/cramFile/container/index.ts +7 -10
- package/src/cramFile/file.ts +71 -77
- package/src/cramFile/record.ts +3 -3
- package/src/cramFile/sectionParsers.ts +27 -22
- package/src/cramFile/slice/decodeRecord.ts +17 -17
- package/src/cramFile/slice/index.ts +8 -9
- package/src/cramFile/util.ts +24 -5
- package/src/htscodecs/arith_gen.js +33 -296
- package/src/htscodecs/fqzcomp.js +2 -476
- package/src/htscodecs/index.js +9 -11
- package/src/htscodecs/iostream.js +3 -2
- package/src/htscodecs/rans.js +3 -315
- package/src/htscodecs/rans4x16.js +6 -557
- package/src/htscodecs/tok3.js +18 -1
- package/src/index.ts +1 -1
- package/src/indexedCramFile.ts +6 -5
- package/src/io/index.ts +5 -4
- package/src/rans/constants.ts +1 -1
- package/src/rans/d04.ts +0 -1
- package/src/rans/decoding.ts +0 -1
- package/src/rans/frequencies.ts +0 -1
- package/src/rans/index.ts +5 -7
- package/src/unzip.ts +5 -1
- package/dist/cramFile/filehandle.d.ts +0 -1
- package/dist/cramFile/filehandle.js +0 -3
- package/dist/cramFile/filehandle.js.map +0 -1
- package/dist/htscodecs/main_arith_gen.d.ts +0 -1
- package/dist/htscodecs/main_arith_gen.js +0 -86
- package/dist/htscodecs/main_arith_gen.js.map +0 -1
- package/dist/htscodecs/main_fqzcomp.d.ts +0 -1
- package/dist/htscodecs/main_fqzcomp.js +0 -112
- package/dist/htscodecs/main_fqzcomp.js.map +0 -1
- package/dist/htscodecs/main_rans.d.ts +0 -1
- package/dist/htscodecs/main_rans.js +0 -83
- package/dist/htscodecs/main_rans.js.map +0 -1
- package/dist/htscodecs/main_rans4x16.d.ts +0 -1
- package/dist/htscodecs/main_rans4x16.js +0 -82
- package/dist/htscodecs/main_rans4x16.js.map +0 -1
- package/dist/htscodecs/main_tok3.d.ts +0 -1
- package/dist/htscodecs/main_tok3.js +0 -84
- package/dist/htscodecs/main_tok3.js.map +0 -1
- package/dist/unzip-pako.d.ts +0 -2
- package/dist/unzip-pako.js +0 -9
- package/dist/unzip-pako.js.map +0 -1
- package/esm/cramFile/filehandle.d.ts +0 -1
- package/esm/cramFile/filehandle.js +0 -2
- package/esm/cramFile/filehandle.js.map +0 -1
- package/esm/htscodecs/main_arith_gen.d.ts +0 -1
- package/esm/htscodecs/main_arith_gen.js +0 -86
- package/esm/htscodecs/main_arith_gen.js.map +0 -1
- package/esm/htscodecs/main_fqzcomp.d.ts +0 -1
- package/esm/htscodecs/main_fqzcomp.js +0 -112
- package/esm/htscodecs/main_fqzcomp.js.map +0 -1
- package/esm/htscodecs/main_rans.d.ts +0 -1
- package/esm/htscodecs/main_rans.js +0 -83
- package/esm/htscodecs/main_rans.js.map +0 -1
- package/esm/htscodecs/main_rans4x16.d.ts +0 -1
- package/esm/htscodecs/main_rans4x16.js +0 -82
- package/esm/htscodecs/main_rans4x16.js.map +0 -1
- package/esm/htscodecs/main_tok3.d.ts +0 -1
- package/esm/htscodecs/main_tok3.js +0 -84
- package/esm/htscodecs/main_tok3.js.map +0 -1
- package/esm/unzip-pako.d.ts +0 -2
- package/esm/unzip-pako.js +0 -6
- package/esm/unzip-pako.js.map +0 -1
- package/src/cramFile/filehandle.ts +0 -1
- package/src/htscodecs/Makefile +0 -142
- package/src/htscodecs/README.md +0 -64
- package/src/htscodecs/main_arith_gen.js +0 -96
- package/src/htscodecs/main_fqzcomp.js +0 -113
- package/src/htscodecs/main_rans.js +0 -88
- package/src/htscodecs/main_rans4x16.js +0 -87
- package/src/htscodecs/main_tok3.js +0 -86
- package/src/unzip-pako.ts +0 -6
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+
{"version":3,"file":"frequencies.js","sourceRoot":"","sources":["../../src/rans/frequencies.ts"],"names":[],"mappings":";;;;;AAWA,kCA0CC;AAED,kCAiEC;AAxHD,cAAc;AACd,sCAA8C;AAC9C,2CAAqC;AACrC,0DAAiC;AAEjC,SAAS,MAAM,CAAC,MAAM;IACpB,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,MAAM,IAAI,2BAAkB,CAAC,kBAAkB,CAAC,CAAA;IAClD,CAAC;AACH,CAAC;AAED,SAAgB,WAAW;AACzB,gBAAgB,CAAC,EAAE;AACnB,yBAAyB,CAAC,OAAO;AACjC,8BAA8B,CAAC,IAAI;IAEnC,2CAA2C;IAC3C,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;IACvB,GAAG,CAAC;QACF,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;YAC1B,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,EAAE,EAAE,CAAA;QACnC,CAAC;QACD,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;QACjC,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,CAAC;YAC3B,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAA;YACvB,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAC,CAAA;QACtE,CAAC;QACD,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnB,kBAAQ,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAE9D,gCAAgC;QAChC,IAAI,CAAC,OAAO,CAAC,CAAC,EAAE,CAAC;YACf,OAAO,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,mBAAO,CAAC,CAAA;QAChC,CAAC;QACD,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEzC,CAAC,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEpB,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE,CAAC;YAChE,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;YACnB,GAAG,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;QACvB,CAAC;aAAM,IAAI,GAAG,KAAK,CAAC,EAAE,CAAC;YACrB,GAAG,IAAI,CAAC,CAAA;YACR,CAAC,IAAI,CAAC,CAAA;QACR,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;QACrB,CAAC;IACH,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAC;IAEjB,MAAM,CAAC,CAAC,GAAG,mBAAO,CAAC,CAAA;AACrB,CAAC;AAED,SAAgB,WAAW;AACzB,gBAAgB,CAAC,EAAE;AACnB,4BAA4B,CAAC,CAAC;AAC9B,gCAAgC,CAAC,IAAI;IAErC,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,IAAI,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;IACvB,GAAG,CAAC;QACF,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;QACvB,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;YACjB,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,UAAU,EAAE,CAAA;QAClC,CAAC;QACD,GAAG,CAAC;YACF,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;gBACvB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,EAAE,EAAE,CAAA;YAChC,CAAC;YACD,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YAC9B,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,CAAC;gBACxB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAA;gBACpB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;YAChE,CAAC;YACD,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAEhB,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;gBACvB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,mBAAO,CAAA;YACxB,CAAC;YAED,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;gBACvB,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,aAAa,EAAE,CAAA;YAC3C,CAAC;YAED,kBAAQ,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAE3D,gCAAgC;YAChC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;gBACnB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,mBAAO,CAAC,CAAA;YAC7B,CAAC;YACD,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAEnC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YACjB,MAAM,CAAC,CAAC,IAAI,mBAAO,CAAC,CAAA;YAEpB,IAAI,IAAI,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE,CAAC;gBACjE,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;gBACnB,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YACxB,CAAC;iBAAM,IAAI,IAAI,KAAK,CAAC,EAAE,CAAC;gBACtB,IAAI,IAAI,CAAC,CAAA;gBACT,CAAC,IAAI,CAAC,CAAA;YACR,CAAC;iBAAM,CAAC;gBACN,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YACrB,CAAC;QACH,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAC;QAEjB,IAAI,IAAI,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE,CAAC;YACjE,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YACnB,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;QACxB,CAAC;aAAM,IAAI,IAAI,KAAK,CAAC,EAAE,CAAC;YACtB,IAAI,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/dist/rans/index.js
CHANGED
|
@@ -5,12 +5,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
exports.default = uncompress;
|
|
7
7
|
// @ts-nocheck
|
|
8
|
-
const buffer_1 = require("buffer");
|
|
9
8
|
const errors_1 = require("../errors");
|
|
10
|
-
const decoding_1 = __importDefault(require("./decoding"));
|
|
11
|
-
const frequencies_1 = require("./frequencies");
|
|
12
9
|
const d04_1 = __importDefault(require("./d04"));
|
|
13
10
|
const d14_1 = __importDefault(require("./d14"));
|
|
11
|
+
const decoding_1 = __importDefault(require("./decoding"));
|
|
12
|
+
const frequencies_1 = require("./frequencies");
|
|
14
13
|
// const /* int */ ORDER_BYTE_LENGTH = 1
|
|
15
14
|
// const /* int */ COMPRESSED_BYTE_LENGTH = 4
|
|
16
15
|
const /* int */ RAW_BYTE_LENGTH = 4;
|
|
@@ -130,6 +129,7 @@ function uncompressOrder1Way4(
|
|
|
130
129
|
class ByteBuffer {
|
|
131
130
|
constructor(nodeBuffer, initialInputPosition = 0) {
|
|
132
131
|
this._buffer = nodeBuffer;
|
|
132
|
+
this._dataView = new DataView(nodeBuffer.buffer);
|
|
133
133
|
this._position = initialInputPosition;
|
|
134
134
|
this.length = nodeBuffer.length;
|
|
135
135
|
}
|
|
@@ -161,7 +161,7 @@ class ByteBuffer {
|
|
|
161
161
|
return pos;
|
|
162
162
|
}
|
|
163
163
|
getInt() {
|
|
164
|
-
const i = this.
|
|
164
|
+
const i = this._dataView.getInt32(this._position, true);
|
|
165
165
|
this._position += 4;
|
|
166
166
|
return i;
|
|
167
167
|
}
|
|
@@ -186,7 +186,7 @@ function uncompress(inputBuffer, outputBuffer, initialInputPosition = 0) {
|
|
|
186
186
|
throw new errors_1.CramMalformedError('Incorrect input length.');
|
|
187
187
|
}
|
|
188
188
|
const /* int */ outputSize = input.getInt();
|
|
189
|
-
const output = new ByteBuffer(outputBuffer ||
|
|
189
|
+
const output = new ByteBuffer(outputBuffer || new Uint8Array(outputSize));
|
|
190
190
|
// TODO output.limit(outputSize)
|
|
191
191
|
if (output.length < outputSize) {
|
|
192
192
|
throw new errors_1.CramMalformedError(`Output buffer too small to fit ${outputSize} bytes.`);
|
package/dist/rans/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/rans/index.ts"],"names":[],"mappings":";;;;;
|
|
1
|
+
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|
package/dist/unzip.d.ts
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
export
|
|
1
|
+
export declare function unzip(input: Uint8Array): Uint8Array<ArrayBufferLike>;
|
package/dist/unzip.js
CHANGED
|
@@ -1,6 +1,8 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.unzip =
|
|
4
|
-
|
|
5
|
-
|
|
3
|
+
exports.unzip = unzip;
|
|
4
|
+
const pako_1 = require("pako");
|
|
5
|
+
function unzip(input) {
|
|
6
|
+
return (0, pako_1.inflate)(input);
|
|
7
|
+
}
|
|
6
8
|
//# sourceMappingURL=unzip.js.map
|
package/dist/unzip.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;AAEA,sBAEC;AAJD,+BAA8B;AAE9B,SAAgB,KAAK,CAAC,KAAiB;IACrC,OAAO,IAAA,cAAO,EAAC,KAAK,CAAC,CAAA;AACvB,CAAC"}
|
package/esm/craiIndex.js
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
|
-
import { unzip } from './unzip';
|
|
2
|
-
import { open } from './io';
|
|
3
1
|
import { CramMalformedError } from './errors';
|
|
4
|
-
|
|
2
|
+
import { open } from './io';
|
|
3
|
+
import { unzip } from './unzip';
|
|
4
|
+
const BAI_MAGIC = 21_578_050; // BAI\1
|
|
5
5
|
function addRecordToIndex(index, record) {
|
|
6
6
|
const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record;
|
|
7
7
|
const s = seqId;
|
|
@@ -17,10 +17,7 @@ function addRecordToIndex(index, record) {
|
|
|
17
17
|
});
|
|
18
18
|
}
|
|
19
19
|
function maybeUnzip(data) {
|
|
20
|
-
|
|
21
|
-
return unzip(data);
|
|
22
|
-
}
|
|
23
|
-
return data;
|
|
20
|
+
return data[0] === 31 && data[1] === 139 ? unzip(data) : data;
|
|
24
21
|
}
|
|
25
22
|
export default class CraiIndex {
|
|
26
23
|
/**
|
|
@@ -36,14 +33,15 @@ export default class CraiIndex {
|
|
|
36
33
|
async parseIndex() {
|
|
37
34
|
const index = {};
|
|
38
35
|
const uncompressedBuffer = maybeUnzip(await this.filehandle.readFile());
|
|
36
|
+
const dataView = new DataView(uncompressedBuffer.buffer);
|
|
39
37
|
if (uncompressedBuffer.length > 4 &&
|
|
40
|
-
|
|
38
|
+
dataView.getUint32(0, true) === BAI_MAGIC) {
|
|
41
39
|
throw new CramMalformedError('invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support');
|
|
42
40
|
}
|
|
43
|
-
// interpret the text as regular ascii, since it is
|
|
44
|
-
//
|
|
45
|
-
//
|
|
46
|
-
//
|
|
41
|
+
// interpret the text as regular ascii, since it is supposed to be only
|
|
42
|
+
// digits and whitespace characters this is written in a deliberately
|
|
43
|
+
// low-level fashion for performance, because some .crai files can be
|
|
44
|
+
// pretty large.
|
|
47
45
|
let currentRecord = [];
|
|
48
46
|
let currentString = '';
|
|
49
47
|
for (const charCode of uncompressedBuffer) {
|
package/esm/craiIndex.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,kBAAkB,EAAE,MAAM,UAAU,CAAA;AAC7C,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAC3B,OAAO,EAAE,KAAK,EAAE,MAAM,SAAS,CAAA;AAI/B,MAAM,SAAS,GAAG,UAAU,CAAA,CAAC,QAAQ;AAYrC,SAAS,gBAAgB,CAAC,KAAkB,EAAE,MAAgB;IAC5D,MAAM,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,cAAc,EAAE,UAAU,EAAE,UAAU,CAAC,GAAG,MAAM,CAAA;IAE3E,MAAM,CAAC,GAAG,KAAM,CAAA;IAChB,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;QACd,KAAK,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;IACf,CAAC;IAED,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;QACZ,KAAK,EAAE,KAAM;QACb,IAAI,EAAE,IAAK;QACX,cAAc,EAAE,cAAe;QAC/B,UAAU,EAAE,UAAW;QACvB,UAAU,EAAE,UAAW;KACxB,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,UAAU,CAAC,IAAgB;IAClC,OAAO,IAAI,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;AAC/D,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,SAAS;IAiB5B;;;;;;OAMG;IACH,YAAY,IAAoB;QAC9B,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;IAC9D,CAAC;IAED,KAAK,CAAC,UAAU;QACd,MAAM,KAAK,GAAgB,EAAE,CAAA;QAC7B,MAAM,kBAAkB,GAAG,UAAU,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAC,CAAA;QACvE,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAA;QACxD,IACE,kBAAkB,CAAC,MAAM,GAAG,CAAC;YAC7B,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EACzC,CAAC;YACD,MAAM,IAAI,kBAAkB,CAC1B,+IAA+I,CAChJ,CAAA;QACH,CAAC;QACD,uEAAuE;QACvE,qEAAqE;QACrE,qEAAqE;QACrE,gBAAgB;QAChB,IAAI,aAAa,GAAa,EAAE,CAAA;QAChC,IAAI,aAAa,GAAG,EAAE,CAAA;QACtB,KAAK,MAAM,QAAQ,IAAI,kBAAkB,EAAE,CAAC;YAC1C,IACE,CAAC,QAAQ,IAAI,EAAE,IAAI,QAAQ,IAAI,EAAE,CAAC,CAAC,SAAS;gBAC5C,CAAC,CAAC,aAAa,IAAI,QAAQ,KAAK,EAAE,CAAC,CAAC,eAAe,EACnD,CAAC;gBACD,aAAa,IAAI,MAAM,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAA;YAChD,CAAC;iBAAM,IAAI,QAAQ,KAAK,CAAC,CAAC,QAAQ,EAAE,CAAC;gBACnC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;gBACtD,aAAa,GAAG,EAAE,CAAA;YACpB,CAAC;iBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,EAAE,CAAC;gBACpC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;gBACtD,aAAa,GAAG,EAAE,CAAA;gBAClB,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;gBACtC,aAAa,GAAG,EAAE,CAAA;YACpB,CAAC;iBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,IAAI,QAAQ,KAAK,EAAE,CAAC,WAAW,EAAE,CAAC;gBACnE,oDAAoD;gBACpD,oCAAoC;gBACpC,MAAM,IAAI,kBAAkB,CAAC,0BAA0B,CAAC,CAAA;YAC1D,CAAC;QACH,CAAC;QAED,8DAA8D;QAC9D,IAAI,aAAa,EAAE,CAAC;YAClB,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;QACxD,CAAC;QACD,IAAI,aAAa,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC/B,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;QACxC,CAAC;QAED,6BAA6B;QAC7B,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,EAAE;YAC7C,MAAM,EAAE,GAAG,GAAI,CAAA;YACf,KAAK,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAA;QACxE,CAAC,CAAC,CAAA;QACF,OAAO,KAAK,CAAA;IACd,CAAC;IAED,QAAQ;QACN,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC;YACtB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACxD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,2BAA2B,CAAC,KAAa;QAC7C,OAAO,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;IACzC,CAAC;IAED;;;;;;;;;;OAUG;IACH,KAAK,CAAC,kBAAkB,CACtB,KAAa,EACb,UAAkB,EAClB,QAAgB;QAEhB,MAAM,UAAU,GAAG,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;QACjD,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,OAAO,GAAG,CAAC,KAAY,EAAE,EAAE;YAC/B,MAAM,UAAU,GAAG,KAAK,CAAC,KAAK,CAAA;YAC9B,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,IAAI,CAAA;YACzC,IAAI,UAAU,GAAG,QAAQ,EAAE,CAAC;gBAC1B,OAAO,CAAC,CAAC,CAAA;YACX,CAAC,CAAC,0BAA0B;YAC5B,IAAI,QAAQ,IAAI,UAAU,EAAE,CAAC;gBAC3B,OAAO,CAAC,CAAA;YACV,CAAC,CAAC,wBAAwB;YAC1B,OAAO,CAAC,CAAA,CAAC,uBAAuB;QAClC,CAAC,CAAA;QACD,MAAM,IAAI,GAAG,EAAa,CAAA;QAC1B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;YAC/B,IAAI,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;gBACzB,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAClB,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import CramCodec, { Cursors } from './_base';
|
|
2
|
-
import CramSlice from '../slice';
|
|
3
|
-
import { CramFileBlock } from '../file';
|
|
4
2
|
import { BetaEncoding } from '../encoding';
|
|
3
|
+
import { CramFileBlock } from '../file';
|
|
4
|
+
import CramSlice from '../slice';
|
|
5
5
|
export default class BetaCodec extends CramCodec<'int', BetaEncoding['parameters']> {
|
|
6
6
|
constructor(parameters: BetaEncoding['parameters'], dataType: 'int');
|
|
7
7
|
decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
|
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import { CramUnimplementedError } from '../../errors';
|
|
2
1
|
import CramCodec from './_base';
|
|
3
2
|
import { getBits } from './getBits';
|
|
3
|
+
import { CramUnimplementedError } from '../../errors';
|
|
4
4
|
export default class BetaCodec extends CramCodec {
|
|
5
5
|
constructor(parameters, dataType) {
|
|
6
6
|
super(parameters, dataType);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":"AAAA,OAAO,
|
|
1
|
+
{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAKrD,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,SAGtC;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,sBAAsB,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,OAAO,CACtB,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"}
|
|
@@ -1,13 +1,13 @@
|
|
|
1
1
|
import CramCodec, { Cursors } from './_base';
|
|
2
2
|
import { ByteArrayLengthEncoding, CramEncoding } from '../encoding';
|
|
3
|
-
import CramSlice from '../slice';
|
|
4
3
|
import { CramFileBlock } from '../file';
|
|
4
|
+
import CramSlice from '../slice';
|
|
5
5
|
import { DataType } from './dataSeriesTypes';
|
|
6
6
|
type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
|
|
7
7
|
export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayLengthEncoding['parameters']> {
|
|
8
8
|
private instantiateCodec;
|
|
9
9
|
constructor(parameters: ByteArrayLengthEncoding['parameters'], dataType: 'byteArray', instantiateCodec: CramCodecFactory);
|
|
10
|
-
decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array
|
|
10
|
+
decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array<ArrayBuffer>;
|
|
11
11
|
_getLengthCodec(): CramCodec<"int", unknown>;
|
|
12
12
|
_getDataCodec(): CramCodec<"byte", unknown>;
|
|
13
13
|
}
|
|
@@ -1,8 +1,8 @@
|
|
|
1
1
|
import CramCodec, { Cursor, Cursors } from './_base';
|
|
2
|
-
import CramSlice from '../slice';
|
|
3
|
-
import { CramFileBlock } from '../file';
|
|
4
2
|
import { ByteArrayStopCramEncoding } from '../encoding';
|
|
3
|
+
import { CramFileBlock } from '../file';
|
|
4
|
+
import CramSlice from '../slice';
|
|
5
5
|
export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayStopCramEncoding['parameters']> {
|
|
6
|
-
decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors):
|
|
7
|
-
_decodeByteArray(contentBlock: CramFileBlock, cursor: Cursor):
|
|
6
|
+
decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array<ArrayBufferLike>;
|
|
7
|
+
_decodeByteArray(contentBlock: CramFileBlock, cursor: Cursor): Uint8Array<ArrayBufferLike>;
|
|
8
8
|
}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import { CramMalformedError } from '../../errors';
|
|
2
1
|
import CramCodec from './_base';
|
|
2
|
+
import { CramMalformedError } from '../../errors';
|
|
3
3
|
import { CramBufferOverrunError } from './getBits';
|
|
4
4
|
export default class ByteArrayStopCodec extends CramCodec {
|
|
5
5
|
decode(slice, coreDataBlock, blocksByContentId, cursors) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.ts"],"names":[],"mappings":"AAAA,OAAO,
|
|
1
|
+
{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.ts"],"names":[],"mappings":"AAAA,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AAIjD,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/C;IACC,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,kBAAkB,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,sBAAsB,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"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import CramCodec, { Cursor, Cursors } from './_base';
|
|
2
|
-
import CramSlice from '../slice';
|
|
3
2
|
import { CramFileBlock } from '../file';
|
|
3
|
+
import CramSlice from '../slice';
|
|
4
4
|
import { ExternalCramEncoding } from '../encoding';
|
|
5
5
|
export default class ExternalCodec extends CramCodec<'int' | 'byte', ExternalCramEncoding['parameters']> {
|
|
6
6
|
private readonly _decodeData;
|
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import { CramMalformedError, CramUnimplementedError } from '../../errors';
|
|
2
1
|
import CramCodec from './_base';
|
|
2
|
+
import { CramMalformedError, CramUnimplementedError } from '../../errors';
|
|
3
3
|
import { parseItf8 } from '../util';
|
|
4
4
|
import { CramBufferOverrunError } from './getBits';
|
|
5
5
|
export default class ExternalCodec extends CramCodec {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;
|
|
1
|
+
{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,kBAAkB,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAGzE,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;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,sBAAsB,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,kBAAkB,CAC1B,kCAAkC,cAAc,GAAG,CACpD,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,SAAS,CACnC,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,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;IACrD,CAAC;CACF"}
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import CramCodec, { Cursors } from './_base';
|
|
2
2
|
import { GammaEncoding } from '../encoding';
|
|
3
|
-
import CramSlice from '../slice';
|
|
4
3
|
import { CramFileBlock } from '../file';
|
|
4
|
+
import CramSlice from '../slice';
|
|
5
5
|
export default class GammaCodec extends CramCodec<'int', GammaEncoding['parameters']> {
|
|
6
6
|
constructor(parameters: GammaEncoding['parameters'], dataType: 'int');
|
|
7
7
|
decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
|
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import { CramUnimplementedError } from '../../errors';
|
|
2
1
|
import CramCodec from './_base';
|
|
3
2
|
import { getBits } from './getBits';
|
|
3
|
+
import { CramUnimplementedError } from '../../errors';
|
|
4
4
|
export default class GammaCodec extends CramCodec {
|
|
5
5
|
constructor(parameters, dataType) {
|
|
6
6
|
super(parameters, dataType);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":"AAAA,OAAO,
|
|
1
|
+
{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAKrD,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAGvC;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,sBAAsB,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,OAAO,CAAC,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,OAAO,CACtB,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"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":"AAAA,MAAM,OAAO,sBAAuB,SAAQ,KAAK;CAAG;AAEpD,MAAM,UAAU,OAAO,CACrB,
|
|
1
|
+
{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":"AAAA,MAAM,OAAO,sBAAuB,SAAQ,KAAK;CAAG;AAEpD,MAAM,UAAU,OAAO,CACrB,IAAgB,EAChB,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,CAAE,IAAI,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QAC7D,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"}
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import CramCodec, { Cursor, Cursors } from './_base';
|
|
2
2
|
import { HuffmanEncoding } from '../encoding';
|
|
3
|
-
import CramSlice from '../slice';
|
|
4
3
|
import { CramFileBlock } from '../file';
|
|
4
|
+
import CramSlice from '../slice';
|
|
5
5
|
export default class HuffmanIntCodec extends CramCodec<'byte' | 'int', HuffmanEncoding['parameters']> {
|
|
6
6
|
private codes;
|
|
7
7
|
private codeBook;
|
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import { CramMalformedError } from '../../errors';
|
|
2
1
|
import CramCodec from './_base';
|
|
3
2
|
import { getBits } from './getBits';
|
|
3
|
+
import { CramMalformedError } from '../../errors';
|
|
4
4
|
function numberOfSetBits(ii) {
|
|
5
5
|
let i = (ii - (ii >> 1)) & 0x55555555;
|
|
6
6
|
i = (i & 0x33333333) + ((i >> 2) & 0x33333333);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"huffman.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/huffman.ts"],"names":[],"mappings":"AAAA,OAAO,
|
|
1
|
+
{"version":3,"file":"huffman.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/huffman.ts"],"names":[],"mappings":"AAAA,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AACnC,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AAKjD,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;AAQD,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,SAG5C;IASC,YACE,UAAyC,EACzC,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAZrB,UAAK,GAAyB,EAAE,CAAA;QAChC,aAAQ,GAA6B,EAAE,CAAA;QACvC,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,CAAC;YAC7C,MAAM,IAAI,SAAS,CACjB,GAAG,IAAI,CAAC,QAAQ,oDAAoD,CACrE,CAAA;QACH,CAAC;QAED,IAAI,CAAC,aAAa,EAAE,CAAA;QACpB,IAAI,CAAC,UAAU,EAAE,CAAA;QACjB,IAAI,CAAC,WAAW,EAAE,CAAA;QAElB,qEAAqE;QACrE,WAAW;QACX,IAAI,IAAI,CAAC,WAAW,CAAC,CAAC,CAAE,CAAC,SAAS,KAAK,CAAC,EAAE,CAAC;YACzC,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,qBAAqB,CAAA;QAC3C,CAAC;IACH,CAAC;IAED,aAAa;QACX,8DAA8D;QAC9D,IAAI,KAAK,GAAG,IAAI,KAAK,CACnB,IAAI,CAAC,UAAU,CAAC,QAAQ,CACzB,CAAA;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClD,KAAK,CAAC,CAAC,CAAC,GAAG;gBACT,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAE;gBACnC,SAAS,EAAE,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,CAAC,CAAE;aAC1C,CAAA;QACH,CAAC;QACD,gDAAgD;QAChD,KAAK,GAAG,KAAK,CAAC,IAAI,CAChB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,MAAM,CAC3D,CAAA;QAED,IAAI,CAAC,QAAQ,GAAG,EAAE,CAAA;QAClB,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;YACnB,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;gBACnC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,CAAA;YACpC,CAAC;YACD,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAE,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAClD,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,UAAU;QACR,IAAI,CAAC,KAAK,GAAG,EAAE,CAAA,CAAC,8CAA8C;QAC9D,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,IAAI,SAAS,GAAG,CAAC,CAAC,CAAA;QAClB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,EAAE,OAAO,CAAC,EAAE,EAAE;YAC7D,MAAM,YAAY,GAAG,MAAM,CAAC,QAAQ,CAAC,SAAS,EAAE,EAAE,CAAC,CAAA;YACnD,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;gBACvB,MAAM,IAAI,GAAG;oBACX,SAAS,EAAE,YAAY;oBACvB,KAAK,EAAE,MAAM;oBACb,OAAO,EAAE,CAAC;iBACX,CAAA;gBACD,SAAS,GAAG,SAAS,GAAG,CAAC,CAAA;gBACzB,MAAM,KAAK,GAAG,YAAY,GAAG,UAAU,CAAA,CAAC,cAAc;gBACtD,SAAS,GAAG,SAAS,IAAI,KAAK,CAAA,CAAC,eAAe;gBAC9C,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA,CAAC,2BAA2B;gBACpD,UAAU,GAAG,UAAU,GAAG,KAAK,CAAA,CAAC,6BAA6B;gBAE7D,IAAI,eAAe,CAAC,SAAS,CAAC,GAAG,YAAY,EAAE,CAAC;oBAC9C,MAAM,IAAI,kBAAkB,CAAC,qBAAqB,CAAC,CAAA;gBACrD,CAAC;gBAED,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,IAAI,CAAA;YAC3B,CAAC,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,WAAW;QACT,IAAI,CAAC,WAAW,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,CAC/C,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,OAAO,CAC7D,CAAA;QAED,IAAI,CAAC,qBAAqB,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;QAC/D,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;QAC1D,IAAI,CAAC,yBAAyB,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAA;QACvE,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,cAAc,CAAC,CAAA;QAEnD,IAAI,CAAC,cAAc,GAAG,IAAI,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACvD,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACvD,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,OAAO,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,aAAa,EAAE,OAAO,CAAC,SAAS,CAAC,CAAA;IAC9D,CAAC;IAED,kBAAkB;IAClB,cAAc;IACd,IAAI;IAEJ,yCAAyC;IACzC,qBAAqB;QACnB,OAAO,IAAI,CAAC,WAAW,CAAC,CAAC,CAAE,CAAC,KAAK,CAAA;IACnC,CAAC;IAED,OAAO,CAAC,KAAgB,EAAE,aAA4B,EAAE,UAAkB;QACxE,MAAM,KAAK,GAAG,aAAa,CAAC,OAAO,CAAA;QAEnC,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACpD,MAAM,MAAM,GAAG,IAAI,CAAC,WAAW,CAAC,CAAC,CAAE,CAAC,SAAS,CAAA;YAC7C,IAAI,KAAK,MAAM,GAAG,OAAO,CAAA;YACzB,IAAI,IAAI,OAAO,CAAC,KAAK,EAAE,UAAU,EAAE,MAAM,GAAG,OAAO,CAAC,CAAA;YACpD,OAAO,GAAG,MAAM,CAAA;YAChB,CAAC;gBACC,MAAM,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,IAAI,CAAE,CAAA;gBACxC,IAAI,KAAK,GAAG,CAAC,CAAC,IAAI,IAAI,CAAC,yBAAyB,CAAC,KAAK,CAAC,KAAK,MAAM,EAAE,CAAC;oBACnE,OAAO,IAAI,CAAC,qBAAqB,CAAC,KAAK,CAAE,CAAA;gBAC3C,CAAC;gBAED,KACE,IAAI,CAAC,GAAG,CAAC,EACT,IAAI,CAAC,WAAW,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,SAAS,KAAK,MAAM;oBAC7C,CAAC,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,EAC3B,CAAC,IAAI,CAAC,EACN,CAAC;oBACD,CAAC,IAAI,CAAC,CAAA;gBACR,CAAC;YACH,CAAC;QACH,CAAC;QACD,MAAM,IAAI,kBAAkB,CAAC,2BAA2B,CAAC,CAAA;IAC3D,CAAC;CACF"}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
1
|
import CramCodec from './_base';
|
|
2
|
-
import { CramEncoding } from '../encoding';
|
|
3
2
|
import { DataType } from './dataSeriesTypes';
|
|
3
|
+
import { CramEncoding } from '../encoding';
|
|
4
4
|
export declare function instantiateCodec<TResult extends DataType = DataType>(encodingData: CramEncoding, dataType: DataType | 'ignore'): CramCodec<TResult>;
|
|
@@ -1,11 +1,11 @@
|
|
|
1
|
-
import { CramUnimplementedError } from '../../errors';
|
|
2
|
-
import HuffmanIntCodec from './huffman';
|
|
3
|
-
import ExternalCodec from './external';
|
|
4
|
-
import ByteArrayStopCodec from './byteArrayStop';
|
|
5
|
-
import ByteArrayLengthCodec from './byteArrayLength';
|
|
6
1
|
import BetaCodec from './beta';
|
|
2
|
+
import ByteArrayLengthCodec from './byteArrayLength';
|
|
3
|
+
import ByteArrayStopCodec from './byteArrayStop';
|
|
4
|
+
import ExternalCodec from './external';
|
|
7
5
|
import GammaCodec from './gamma';
|
|
6
|
+
import HuffmanIntCodec from './huffman';
|
|
8
7
|
import SubexpCodec from './subexp';
|
|
8
|
+
import { CramUnimplementedError } from '../../errors';
|
|
9
9
|
const codecClasses = {
|
|
10
10
|
1: ExternalCodec,
|
|
11
11
|
// 2: GolombCodec,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/index.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,QAAQ,CAAA;AAC9B,OAAO,oBAAoB,MAAM,mBAAmB,CAAA;AACpD,OAAO,kBAAkB,MAAM,iBAAiB,CAAA;AAEhD,OAAO,aAAa,MAAM,YAAY,CAAA;AACtC,OAAO,UAAU,MAAM,SAAS,CAAA;AAChC,OAAO,eAAe,MAAM,WAAW,CAAA;AACvC,OAAO,WAAW,MAAM,UAAU,CAAA;AAClC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAGrD,MAAM,YAAY,GAAG;IACnB,CAAC,EAAE,aAAa;IAChB,kBAAkB;IAClB,CAAC,EAAE,eAAe;IAClB,CAAC,EAAE,oBAAoB;IACvB,CAAC,EAAE,kBAAkB;IACrB,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,WAAW;IACd,sBAAsB;IACtB,CAAC,EAAE,UAAU;CACd,CAAA;AAED,SAAS,mBAAmB,CAAC,EAAU;IACrC,OAAQ,YAAoB,CAAC,EAAE,CAAC,CAAA;AAClC,CAAC;AAED,MAAM,UAAU,gBAAgB,CAC9B,YAA0B,EAC1B,QAA6B;IAE7B,MAAM,UAAU,GAAG,mBAAmB,CACpC,QAAQ,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,OAAO,CACjD,CAAA;IACD,IAAI,CAAC,UAAU,EAAE,CAAC;QAChB,MAAM,IAAI,sBAAsB,CAC9B,qCAAqC,YAAY,CAAC,OAAO,EAAE,CAC5D,CAAA;IACH,CAAC;IAED,OAAO,IAAI,UAAU,CAAC,YAAY,CAAC,UAAU,EAAE,QAAQ,EAAE,gBAAgB,CAAC,CAAA;AAC5E,CAAC"}
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import CramCodec, { Cursors } from './_base';
|
|
2
|
-
import CramSlice from '../slice';
|
|
3
|
-
import { CramFileBlock } from '../file';
|
|
4
2
|
import { SubexpEncoding } from '../encoding';
|
|
3
|
+
import { CramFileBlock } from '../file';
|
|
4
|
+
import CramSlice from '../slice';
|
|
5
5
|
export default class SubexpCodec extends CramCodec<'int', SubexpEncoding['parameters']> {
|
|
6
6
|
constructor(parameters: SubexpEncoding['parameters'], dataType: 'int');
|
|
7
7
|
decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
|
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import { CramUnimplementedError } from '../../errors';
|
|
2
1
|
import CramCodec from './_base';
|
|
3
2
|
import { getBits } from './getBits';
|
|
3
|
+
import { CramUnimplementedError } from '../../errors';
|
|
4
4
|
export default class SubexpCodec extends CramCodec {
|
|
5
5
|
constructor(parameters, dataType) {
|
|
6
6
|
super(parameters, dataType);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":"AAAA,OAAO,
|
|
1
|
+
{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAKrD,MAAM,CAAC,OAAO,OAAO,WAAY,SAAQ,SAGxC;IACC,YAAY,UAAwC,EAAE,QAAe;QACnE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,OAAO,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE,CAAC;YAC5D,cAAc,GAAG,cAAc,GAAG,CAAC,CAAA;QACrC,CAAC;QAED,IAAI,CAAS,CAAA;QACb,IAAI,CAAS,CAAA;QACb,IAAI,cAAc,KAAK,CAAC,EAAE,CAAC;YACzB,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QAC1D,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,IAAI,GAAG,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;YACjE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;QACrB,CAAC;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF"}
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import CramCodec from '../codecs/_base';
|
|
2
|
-
import { CramCompressionHeader } from '../sectionParsers';
|
|
3
|
-
import { CramEncoding } from '../encoding';
|
|
4
2
|
import { DataSeriesEncodingKey, DataSeriesEncodingMap } from '../codecs/dataSeriesTypes';
|
|
3
|
+
import { CramEncoding } from '../encoding';
|
|
4
|
+
import { CramCompressionHeader } from '../sectionParsers';
|
|
5
5
|
declare const dataSeriesTypes: {
|
|
6
6
|
readonly BF: "int";
|
|
7
7
|
readonly CF: "int";
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"compressionScheme.js","sourceRoot":"","sources":["../../../src/cramFile/container/compressionScheme.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"compressionScheme.js","sourceRoot":"","sources":["../../../src/cramFile/container/compressionScheme.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,WAAW,CAAA;AAS5C,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,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,OAAO,MAAM,CAAA;AACf,CAAC;AAMD,MAAM,CAAC,OAAO,OAAO,8BAA8B;IAWjD,YAAY,OAA8B;QALnC,yBAAoB,GAAoB,EAAE,CAAA;QAC1C,kBAAa,GAA8B,EAAE,CAAA;QAC7C,gBAAW,GAAiC,EAAE,CAAA;QAInD,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;IACxC,CAAC;IAED;;;OAGG;IACH,cAAc,CAAC,OAAe;QAC5B,MAAM,IAAI,GAAG,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;QACxC,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC9C,IAAI,CAAC,YAAY,EAAE,CAAC;gBAClB,MAAM,IAAI,KAAK,CAAC,wBAAwB,CAAC,CAAA;YAC3C,CAAC;YACD,MAAM,GAAG,GAAG,gBAAgB,CAC1B,YAAY,EACZ,WAAW,CACZ,CAAA;YACD,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,GAAG,CAAA;YACjC,OAAO,GAAG,CAAA;QACZ,CAAC;aAAM,CAAC;YACN,OAAO,IAAI,CAAA;QACb,CAAC;IACH,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,uEAAuE;YACvE,IAAI,YAAY,EAAE,CAAC;gBACjB,MAAM,QAAQ,GAAG,eAAe,CAAC,cAAc,CAAC,CAAA;gBAChD,uEAAuE;gBACvE,IAAI,CAAC,QAAQ,EAAE,CAAC;oBACd,MAAM,IAAI,kBAAkB,CAC1B,oBAAoB,cAAc,yCAAyC,CAC5E,CAAA;gBACH,CAAC;gBACD,CAAC,GAAG,gBAAgB,CAAC,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,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE,CAAC;gBACxB,OAAM;YACR,CAAC;YACD,IAAI,CAAC,CAAC,CAAC,GAAI,IAAY,CAAC,CAAC,CAAC,CAAA;QAC5B,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
|
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
import { Buffer } from 'buffer';
|
|
2
1
|
import CramSlice from '../slice';
|
|
3
2
|
import CramContainerCompressionScheme from './compressionScheme';
|
|
4
3
|
import CramFile from '../file';
|
|
@@ -47,7 +46,7 @@ export default class CramContainer {
|
|
|
47
46
|
_endPosition: number;
|
|
48
47
|
contentPosition: number;
|
|
49
48
|
_size: number;
|
|
50
|
-
content:
|
|
49
|
+
content: Uint8Array;
|
|
51
50
|
crc32?: number;
|
|
52
51
|
} | null | undefined>;
|
|
53
52
|
getFirstBlock(): Promise<import("../file").CramFileBlock | undefined>;
|
|
@@ -1,8 +1,7 @@
|
|
|
1
|
-
import { Buffer } from 'buffer';
|
|
2
1
|
import { CramMalformedError } from '../../errors';
|
|
3
2
|
// locals
|
|
4
|
-
import { itf8Size, parseItem, tinyMemoize } from '../util';
|
|
5
3
|
import CramSlice from '../slice';
|
|
4
|
+
import { itf8Size, parseItem, tinyMemoize } from '../util';
|
|
6
5
|
import CramContainerCompressionScheme from './compressionScheme';
|
|
7
6
|
import { getSectionParsers } from '../sectionParsers';
|
|
8
7
|
export default class CramContainer {
|
|
@@ -17,7 +16,7 @@ export default class CramContainer {
|
|
|
17
16
|
const containerHeader = await this.getHeader();
|
|
18
17
|
// if there are no records in the container, there will be no compression
|
|
19
18
|
// header
|
|
20
|
-
if (!
|
|
19
|
+
if (!containerHeader?.numRecords) {
|
|
21
20
|
return null;
|
|
22
21
|
}
|
|
23
22
|
const { majorVersion } = await this.file.getDefinition();
|
|
@@ -67,8 +66,7 @@ export default class CramContainer {
|
|
|
67
66
|
}
|
|
68
67
|
// parse the container header. do it in 2 pieces because you cannot tell
|
|
69
68
|
// how much to buffer until you read numLandmarks
|
|
70
|
-
const bytes1 =
|
|
71
|
-
await this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position);
|
|
69
|
+
const bytes1 = await this.file.read(cramContainerHeader1.maxLength, position);
|
|
72
70
|
const header1 = parseItem(bytes1, cramContainerHeader1.parser);
|
|
73
71
|
const numLandmarksSize = itf8Size(header1.numLandmarks);
|
|
74
72
|
if (position + header1.length >= fileSize) {
|
|
@@ -76,8 +74,7 @@ export default class CramContainer {
|
|
|
76
74
|
console.warn(`container at ${position} is beyond fileSize:${fileSize}, skipping`);
|
|
77
75
|
return undefined;
|
|
78
76
|
}
|
|
79
|
-
const bytes2 =
|
|
80
|
-
await this.file.read(bytes2, 0, cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
|
|
77
|
+
const bytes2 = await this.file.read(cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
|
|
81
78
|
const header2 = parseItem(bytes2, cramContainerHeader2.parser);
|
|
82
79
|
if (this.file.validateChecksums && header2.crc32 !== undefined) {
|
|
83
80
|
await this.file.checkCrc32(position, header1._size + header2._size - numLandmarksSize - 4, header2.crc32, `container header beginning at position ${position}`);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,
|
|
1
|
+
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