@gmod/cram 3.0.0 → 3.0.1
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/cram-bundle.js +1 -1
- package/dist/cramFile/codecs/byteArrayStop.js +1 -1
- package/dist/cramFile/codecs/huffman.js +1 -1
- package/dist/cramFile/codecs/huffman.js.map +1 -1
- package/dist/cramFile/codecs/subexp.js.map +1 -1
- package/dist/cramFile/container/index.d.ts +1 -0
- package/dist/cramFile/container/index.js +8 -5
- package/dist/cramFile/container/index.js.map +1 -1
- package/dist/cramFile/file.d.ts +1 -0
- package/dist/cramFile/file.js +14 -13
- 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.js.map +1 -1
- package/dist/cramFile/slice/decodeRecord.js +5 -4
- package/dist/cramFile/slice/decodeRecord.js.map +1 -1
- package/dist/cramFile/slice/index.js +2 -2
- package/dist/cramFile/slice/index.js.map +1 -1
- package/dist/cramFile/util.js.map +1 -1
- package/dist/rans/d04.js.map +1 -1
- package/dist/rans/decoding.d.ts +4 -4
- package/dist/rans/decoding.js +5 -6
- package/dist/rans/decoding.js.map +1 -1
- package/dist/rans/index.js +4 -3
- package/dist/rans/index.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayStop.js +1 -1
- package/esm/cramFile/codecs/huffman.js +1 -1
- package/esm/cramFile/codecs/huffman.js.map +1 -1
- package/esm/cramFile/codecs/subexp.js.map +1 -1
- package/esm/cramFile/container/index.d.ts +1 -0
- package/esm/cramFile/container/index.js +6 -3
- package/esm/cramFile/container/index.js.map +1 -1
- package/esm/cramFile/file.d.ts +1 -0
- package/esm/cramFile/file.js +6 -5
- 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.js.map +1 -1
- package/esm/cramFile/slice/decodeRecord.js +5 -4
- package/esm/cramFile/slice/decodeRecord.js.map +1 -1
- package/esm/cramFile/slice/index.js +2 -2
- package/esm/cramFile/slice/index.js.map +1 -1
- package/esm/cramFile/util.js +3 -3
- package/esm/cramFile/util.js.map +1 -1
- package/esm/rans/d04.js.map +1 -1
- package/esm/rans/decoding.d.ts +4 -4
- package/esm/rans/decoding.js +5 -6
- package/esm/rans/decoding.js.map +1 -1
- package/esm/rans/index.js +3 -2
- package/esm/rans/index.js.map +1 -1
- package/package.json +1 -1
- package/src/cramFile/codecs/byteArrayStop.ts +1 -1
- package/src/cramFile/codecs/huffman.ts +1 -1
- package/src/cramFile/codecs/subexp.ts +2 -2
- package/src/cramFile/container/index.ts +6 -6
- package/src/cramFile/declare.d.ts +1 -0
- package/src/cramFile/file.ts +10 -11
- package/src/cramFile/record.ts +3 -6
- package/src/cramFile/sectionParsers.ts +4 -4
- package/src/cramFile/slice/decodeRecord.ts +20 -12
- package/src/cramFile/slice/index.ts +2 -2
- package/src/cramFile/util.ts +5 -5
- package/src/rans/d04.ts +1 -1
- package/src/rans/decoding.ts +5 -7
- package/src/rans/index.ts +3 -2
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1
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+
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package/dist/rans/d04.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"d04.js","sourceRoot":"","sources":["../../src/rans/d04.ts"],"names":[],"mappings":";;;;;AAMA,6BA6EC;AAnFD,aAAa;AACb,sCAA8C;AAE9C,2CAAsC;AACtC,0DAAiC;AAEjC,SAAwB,UAAU;AAChC,gBAAgB,CAAC,KAAK;AACtB,yBAAyB,CAAC,CAAC;AAC3B,uBAAuB,CAAC,IAAI;AAC5B,gBAAgB,CAAC,GAAG;IAEpB,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,UAAU,GAAG,GAAG,CAAC,SAAS,EAAE,CAAA;IAC5C,MAAM,SAAS,CAAC,SAAS,GAAG,UAAU,GAAG,CAAC,CAAC,CAAA;IAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACtC,MAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QACxD,MAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QACxD,MAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QACxD,MAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QAExD,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;QAChB,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;QAEpB,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACpE,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACpE,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACpE,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QAEpE,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;IAC5C,CAAC;IAED,GAAG,CAAC,WAAW,CAAC,SAAS,CAAC,CAAA;IAC1B,IAAI,UAAU,CAAC,CAAS,CAAA;IACxB,QAAQ,UAAU,GAAG,CAAC,EAAE,CAAC;QACvB,KAAK,CAAC;YACJ,MAAK;QACP,KAAK,CAAC;YACJ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACV,MAAK;QAEP,KAAK,CAAC;YACJ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAEV,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACV,MAAK;QAEP,KAAK,CAAC;YACJ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAEV,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAEV,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACV,MAAK;QAEP;YACE,MAAM,IAAI,2BAAkB,CAC1B,sDAAsD,CACvD,CAAA;IACL,CAAC;IAED,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;AACpB,CAAC"}
|
package/dist/rans/decoding.d.ts
CHANGED
|
@@ -4,7 +4,7 @@ declare class FC {
|
|
|
4
4
|
declare class AriDecoder {
|
|
5
5
|
constructor();
|
|
6
6
|
}
|
|
7
|
-
declare class
|
|
7
|
+
declare class DecodingSymbol {
|
|
8
8
|
constructor();
|
|
9
9
|
}
|
|
10
10
|
declare function symbolInit(sym: any, start: any, freq: any): void;
|
|
@@ -13,10 +13,10 @@ declare function advanceSymbolStep(r: any, sym: any, scaleBits: any): number;
|
|
|
13
13
|
declare function get(/* final int */ r: any, /* final int */ scaleBits: any): number;
|
|
14
14
|
declare function advanceSymbol(r: any, pptr: any, sym: any, scaleBits: any): any;
|
|
15
15
|
declare function renormalize(r: any, pptr: any): any;
|
|
16
|
-
declare const
|
|
16
|
+
declare const _default: {
|
|
17
17
|
FC: typeof FC;
|
|
18
18
|
AriDecoder: typeof AriDecoder;
|
|
19
|
-
|
|
19
|
+
DecodingSymbol: typeof DecodingSymbol;
|
|
20
20
|
symbolInit: typeof symbolInit;
|
|
21
21
|
advanceStep: typeof advanceStep;
|
|
22
22
|
advanceSymbolStep: typeof advanceSymbolStep;
|
|
@@ -24,4 +24,4 @@ declare const Decode: {
|
|
|
24
24
|
advanceSymbol: typeof advanceSymbol;
|
|
25
25
|
renormalize: typeof renormalize;
|
|
26
26
|
};
|
|
27
|
-
export default
|
|
27
|
+
export default _default;
|
package/dist/rans/decoding.js
CHANGED
|
@@ -21,7 +21,7 @@ class AriDecoder {
|
|
|
21
21
|
this.R = null;
|
|
22
22
|
}
|
|
23
23
|
}
|
|
24
|
-
class
|
|
24
|
+
class DecodingSymbol {
|
|
25
25
|
// int start; // Start of range.
|
|
26
26
|
// int freq; // Symbol frequency.
|
|
27
27
|
constructor() {
|
|
@@ -32,10 +32,10 @@ class Symbol {
|
|
|
32
32
|
// Initialize a decoder symbol to start "start" and frequency "freq"
|
|
33
33
|
function symbolInit(sym, start, freq) {
|
|
34
34
|
if (!(start <= 1 << 16)) {
|
|
35
|
-
throw new errors_1.CramMalformedError(
|
|
35
|
+
throw new errors_1.CramMalformedError('assertion failed: start <= 1<<16');
|
|
36
36
|
}
|
|
37
37
|
if (!(freq <= (1 << 16) - start)) {
|
|
38
|
-
throw new errors_1.CramMalformedError(
|
|
38
|
+
throw new errors_1.CramMalformedError('assertion failed: freq <= 1<<16');
|
|
39
39
|
}
|
|
40
40
|
sym.start = start;
|
|
41
41
|
sym.freq = freq;
|
|
@@ -106,10 +106,10 @@ function symbolInit(sym, start, freq) {
|
|
|
106
106
|
}
|
|
107
107
|
return r;
|
|
108
108
|
}
|
|
109
|
-
|
|
109
|
+
exports.default = {
|
|
110
110
|
FC,
|
|
111
111
|
AriDecoder,
|
|
112
|
-
|
|
112
|
+
DecodingSymbol,
|
|
113
113
|
symbolInit,
|
|
114
114
|
advanceStep,
|
|
115
115
|
advanceSymbolStep,
|
|
@@ -117,5 +117,4 @@ const Decode = {
|
|
|
117
117
|
advanceSymbol,
|
|
118
118
|
renormalize,
|
|
119
119
|
};
|
|
120
|
-
exports.default = Decode;
|
|
121
120
|
//# sourceMappingURL=decoding.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"decoding.js","sourceRoot":"","sources":["../../src/rans/decoding.ts"],"names":[],"mappings":";;AAAA,aAAa;AACb,sCAA8C;AAE9C,2CAAyC;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,
|
|
1
|
+
{"version":3,"file":"decoding.js","sourceRoot":"","sources":["../../src/rans/decoding.ts"],"names":[],"mappings":";;AAAA,aAAa;AACb,sCAA8C;AAE9C,2CAAyC;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,cAAc;IAClB,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,2BAAkB,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,2BAAkB,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,uBAAW,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,uBAAW,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,uBAAW,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,uBAAW,EAAC;IAC3B,CAAC;IAED,OAAO,CAAC,CAAA;AACV,CAAC;AAED,kBAAe;IACb,EAAE;IACF,UAAU;IACV,cAAc;IACd,UAAU;IACV,WAAW;IACX,iBAAiB;IACjB,GAAG;IACH,aAAa;IACb,WAAW;CACZ,CAAA"}
|
package/dist/rans/index.js
CHANGED
|
@@ -5,6 +5,7 @@ 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");
|
|
8
9
|
const errors_1 = require("../errors");
|
|
9
10
|
const decoding_1 = __importDefault(require("./decoding"));
|
|
10
11
|
const frequencies_1 = require("./frequencies");
|
|
@@ -101,7 +102,7 @@ function uncompressOrder0Way4(
|
|
|
101
102
|
const D = new decoding_1.default.AriDecoder();
|
|
102
103
|
const syms = new Array(256);
|
|
103
104
|
for (let i = 0; i < syms.length; i += 1) {
|
|
104
|
-
syms[i] = new decoding_1.default.
|
|
105
|
+
syms[i] = new decoding_1.default.DecodingSymbol();
|
|
105
106
|
}
|
|
106
107
|
(0, frequencies_1.readStatsO0)(input, D, syms);
|
|
107
108
|
(0, d04_1.default)(input, D, syms, out);
|
|
@@ -118,7 +119,7 @@ function uncompressOrder1Way4(
|
|
|
118
119
|
for (let i = 0; i < syms.length; i += 1) {
|
|
119
120
|
syms[i] = new Array(256);
|
|
120
121
|
for (let j = 0; j < syms[i].length; j += 1) {
|
|
121
|
-
syms[i][j] = new decoding_1.default.
|
|
122
|
+
syms[i][j] = new decoding_1.default.DecodingSymbol();
|
|
122
123
|
}
|
|
123
124
|
}
|
|
124
125
|
(0, frequencies_1.readStatsO1)(input, D, syms);
|
|
@@ -185,7 +186,7 @@ function uncompress(inputBuffer, outputBuffer, initialInputPosition = 0) {
|
|
|
185
186
|
throw new errors_1.CramMalformedError('Incorrect input length.');
|
|
186
187
|
}
|
|
187
188
|
const /* int */ outputSize = input.getInt();
|
|
188
|
-
const output = new ByteBuffer(outputBuffer || Buffer.allocUnsafe(outputSize));
|
|
189
|
+
const output = new ByteBuffer(outputBuffer || buffer_1.Buffer.allocUnsafe(outputSize));
|
|
189
190
|
// TODO output.limit(outputSize)
|
|
190
191
|
if (output.length < outputSize) {
|
|
191
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
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/rans/index.ts"],"names":[],"mappings":";;;;;AA+MA,6BA2CC;AA1PD,aAAa;AACb,mCAA+B;AAC/B,sCAA8C;AAE9C,0DAAiC;AACjC,+CAAwD;AAExD,gDAAuB;AACvB,gDAAuB;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,kBAAQ,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,kBAAQ,CAAC,cAAc,EAAE,CAAA;IACzC,CAAC;IAED,IAAA,yBAAW,EAAC,KAAK,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,IAAA,aAAG,EAAC,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,kBAAQ,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,kBAAQ,CAAC,cAAc,EAAE,CAAA;QAC5C,CAAC;IACH,CAAC;IACD,IAAA,yBAAW,EAAC,KAAK,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,IAAA,aAAG,EAAC,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,SAAwB,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,2BAAkB,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,2BAAkB,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,eAAM,CAAC,WAAW,CAAC,UAAU,CAAC,CAAC,CAAA;IAC7E,gCAAgC;IAEhC,IAAI,MAAM,CAAC,MAAM,GAAG,UAAU,EAAE,CAAC;QAC/B,MAAM,IAAI,2BAAkB,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,2BAAkB,CAAC,uBAAuB,KAAK,EAAE,CAAC,CAAA;IAChE,CAAC;AACH,CAAC"}
|
|
@@ -26,7 +26,7 @@ export default class ByteArrayStopCodec extends CramCodec {
|
|
|
26
26
|
while (dataBuffer[stopPosition] !== stopByte &&
|
|
27
27
|
stopPosition < dataBuffer.length) {
|
|
28
28
|
if (stopPosition === dataBuffer.length) {
|
|
29
|
-
throw new CramBufferOverrunError(
|
|
29
|
+
throw new CramBufferOverrunError('byteArrayStop reading beyond length of data buffer?');
|
|
30
30
|
}
|
|
31
31
|
stopPosition = stopPosition + 1;
|
|
32
32
|
}
|
|
@@ -53,7 +53,7 @@ export default class HuffmanIntCodec extends CramCodec {
|
|
|
53
53
|
let codeLength = 0;
|
|
54
54
|
let codeValue = -1;
|
|
55
55
|
Object.entries(this.codeBook).forEach(([bitLength, symbols]) => {
|
|
56
|
-
const bitLengthInt = parseInt(bitLength, 10);
|
|
56
|
+
const bitLengthInt = Number.parseInt(bitLength, 10);
|
|
57
57
|
symbols.forEach(symbol => {
|
|
58
58
|
const code = {
|
|
59
59
|
bitLength: bitLengthInt,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"huffman.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/huffman.ts"],"names":[],"mappings":"AAAA,sDAAsD;AACtD,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;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;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,CAAC,CAAC,SAAS,KAAK,CAAC,EAAE,CAAC;YACxC,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,IAAI,CAAC,EAAE,CAAC;YACrD,KAAK,CAAC,CAAC,CAAC,GAAG;gBACT,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC;gBAClC,SAAS,EAAE,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,CAAC,CAAC;aACzC,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,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACjD,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,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACtD,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,CAAC,CAAC,KAAK,CAAA;IAClC,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,CAAC,CAAC,SAAS,CAAA;YAC5C,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,CAAC,CAAA;gBACvC,IAAI,KAAK,GAAG,CAAC,CAAC,IAAI,IAAI,CAAC,yBAAyB,CAAC,KAAK,CAAC,KAAK,MAAM,EAAE,CAAC;oBACnE,OAAO,IAAI,CAAC,qBAAqB,CAAC,KAAK,CAAC,CAAA;gBAC1C,CAAC;gBAED,KACE,IAAI,CAAC,GAAG,CAAC,EACT,IAAI,CAAC,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,KAAK,MAAM;oBAC5C,CAAC,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,EAC3B,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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AAKnC,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,
|
|
1
|
+
{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AAKnC,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"}
|
|
@@ -1,4 +1,6 @@
|
|
|
1
|
+
import { Buffer } from 'buffer';
|
|
1
2
|
import { CramMalformedError } from '../../errors';
|
|
3
|
+
// locals
|
|
2
4
|
import { itf8Size, parseItem, tinyMemoize } from '../util';
|
|
3
5
|
import CramSlice from '../slice';
|
|
4
6
|
import CramContainerCompressionScheme from './compressionScheme';
|
|
@@ -25,7 +27,7 @@ export default class CramContainer {
|
|
|
25
27
|
return undefined;
|
|
26
28
|
}
|
|
27
29
|
if (block.contentType !== 'COMPRESSION_HEADER') {
|
|
28
|
-
throw new CramMalformedError(`invalid content type ${block.contentType} in
|
|
30
|
+
throw new CramMalformedError(`invalid content type ${block.contentType} in compression header block`);
|
|
29
31
|
}
|
|
30
32
|
const content = parseItem(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
|
|
31
33
|
return {
|
|
@@ -60,7 +62,7 @@ export default class CramContainer {
|
|
|
60
62
|
const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
|
|
61
63
|
const { size: fileSize } = await this.file.stat();
|
|
62
64
|
if (position >= fileSize) {
|
|
63
|
-
console.warn(`
|
|
65
|
+
console.warn(`pos:${position}>=fileSize:${fileSize} in cram container`);
|
|
64
66
|
return undefined;
|
|
65
67
|
}
|
|
66
68
|
// parse the container header. do it in 2 pieces because you cannot tell
|
|
@@ -70,7 +72,8 @@ export default class CramContainer {
|
|
|
70
72
|
const header1 = parseItem(bytes1, cramContainerHeader1.parser);
|
|
71
73
|
const numLandmarksSize = itf8Size(header1.numLandmarks);
|
|
72
74
|
if (position + header1.length >= fileSize) {
|
|
73
|
-
|
|
75
|
+
// header indicates container goes beyond fileSize
|
|
76
|
+
console.warn(`container at ${position} is beyond fileSize:${fileSize}, skipping`);
|
|
74
77
|
return undefined;
|
|
75
78
|
}
|
|
76
79
|
const bytes2 = Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAC/B,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AACjD,SAAS;AACT,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAC1D,OAAO,SAAS,MAAM,UAAU,CAAA;AAChC,OAAO,8BAA8B,MAAM,qBAAqB,CAAA;AAEhE,OAAO,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAA;AAErD,MAAM,CAAC,OAAO,OAAO,aAAa;IAChC,YACS,IAAc,EACd,YAAoB;QADpB,SAAI,GAAJ,IAAI,CAAU;QACd,iBAAY,GAAZ,YAAY,CAAQ;IAC1B,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IACrD,CAAC;IAED,KAAK,CAAC,yBAAyB;QAC7B,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAE9C,yEAAyE;QACzE,SAAS;QACT,IAAI,CAAC,CAAA,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,UAAU,CAAA,EAAE,CAAC;YACjC,OAAO,IAAI,CAAA;QACb,CAAC;QACD,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,cAAc,GAAG,iBAAiB,CAAC,YAAY,CAAC,CAAA;QAEtD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACxC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,IAAI,KAAK,CAAC,WAAW,KAAK,oBAAoB,EAAE,CAAC;YAC/C,MAAM,IAAI,kBAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,8BAA8B,CACxE,CAAA;QACH,CAAC;QAED,MAAM,OAAO,GAAG,SAAS,CACvB,KAAK,CAAC,OAAO,EACb,cAAc,CAAC,qBAAqB,CAAC,MAAM,EAC3C,CAAC,EACD,KAAK,CAAC,eAAe,CACtB,CAAA;QACD,OAAO;YACL,GAAG,KAAK;YACR,aAAa,EAAE,OAAO;SACvB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC9C,IAAI,CAAC,eAAe,EAAE,CAAC;YACrB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;IAC1D,CAAC;IAED,2EAA2E;IAC3E,SAAS;IACT,KAAK,CAAC,oBAAoB;QACxB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,yBAAyB,EAAE,CAAA;QACrD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,OAAO,IAAI,8BAA8B,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;IACjE,CAAC;IAED,QAAQ,CAAC,aAAqB,EAAE,SAAiB;QAC/C,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,IAAI,SAAS,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,CAAA;IACtD,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,QAAgB;QACzC,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,cAAc,GAAG,iBAAiB,CAAC,YAAY,CAAC,CAAA;QACtD,MAAM,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QACrE,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QAEjD,IAAI,QAAQ,IAAI,QAAQ,EAAE,CAAC;YACzB,OAAO,CAAC,IAAI,CAAC,OAAO,QAAQ,cAAc,QAAQ,oBAAoB,CAAC,CAAA;YACvE,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,wEAAwE;QACxE,iDAAiD;QACjD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,oBAAoB,CAAC,SAAS,CAAC,CAAA;QACjE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,oBAAoB,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;QACzE,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAC9D,MAAM,gBAAgB,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACvD,IAAI,QAAQ,GAAG,OAAO,CAAC,MAAM,IAAI,QAAQ,EAAE,CAAC;YAC1C,kDAAkD;YAClD,OAAO,CAAC,IAAI,CACV,gBAAgB,QAAQ,uBAAuB,QAAQ,YAAY,CACpE,CAAA;YACD,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAC/B,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,CACrD,CAAA;QACD,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;QACD,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAE9D,IAAI,IAAI,CAAC,IAAI,CAAC,iBAAiB,IAAI,OAAO,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;YAC/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;QACH,CAAC;QAED,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,EAAE;YACrD,KAAK,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB;YACvD,YAAY,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,QAAQ;SAC1E,CAAC,CAAA;QAEF,OAAO,cAAc,CAAA;IACvB,CAAC;CACF;AAED,0DAA0D;KACvD,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,aAAa,EAAE,MAAM,CAAC,CAAC,CAAA"}
|
package/esm/cramFile/file.d.ts
CHANGED
package/esm/cramFile/file.js
CHANGED
|
@@ -1,11 +1,12 @@
|
|
|
1
|
-
import {
|
|
1
|
+
import { Buffer } from 'buffer';
|
|
2
2
|
import crc32 from 'buffer-crc32';
|
|
3
3
|
import QuickLRU from 'quick-lru';
|
|
4
4
|
import htscodecs from '@jkbonfield/htscodecs';
|
|
5
|
-
// @ts-expect-error
|
|
6
5
|
import bzip2 from 'bzip2';
|
|
7
6
|
import { XzReadableStream } from 'xz-decompress';
|
|
8
7
|
import { CramMalformedError, CramUnimplementedError } from '../errors';
|
|
8
|
+
// locals
|
|
9
|
+
import { unzip } from '../unzip';
|
|
9
10
|
import ransuncompress from '../rans';
|
|
10
11
|
import { cramFileDefinition, getSectionParsers, } from './sectionParsers';
|
|
11
12
|
import CramContainer from './container';
|
|
@@ -20,7 +21,7 @@ function bufferToStream(buf) {
|
|
|
20
21
|
},
|
|
21
22
|
});
|
|
22
23
|
}
|
|
23
|
-
// source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
|
|
24
|
+
// source: https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
|
|
24
25
|
function getEndianness() {
|
|
25
26
|
const uInt32 = new Uint32Array([0x11223344]);
|
|
26
27
|
const uInt8 = new Uint8Array(uInt32.buffer);
|
|
@@ -228,12 +229,12 @@ export default class CramFile {
|
|
|
228
229
|
let chunk;
|
|
229
230
|
do {
|
|
230
231
|
chunk = bzip2.decompress(bits, size);
|
|
231
|
-
if (chunk
|
|
232
|
+
if (chunk !== -1) {
|
|
232
233
|
Buffer.from(chunk).copy(outputBuffer, j);
|
|
233
234
|
j += chunk.length;
|
|
234
235
|
size -= chunk.length;
|
|
235
236
|
}
|
|
236
|
-
} while (chunk
|
|
237
|
+
} while (chunk !== -1);
|
|
237
238
|
}
|
|
238
239
|
else if (compressionMethod === 'lzma') {
|
|
239
240
|
const decompressedResponse = new Response(new XzReadableStream(bufferToStream(inputBuffer)));
|
package/esm/cramFile/file.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
+
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|
package/esm/cramFile/record.js
CHANGED
|
@@ -158,8 +158,8 @@ export const MateFlags = [
|
|
|
158
158
|
function makeFlagsHelper(x) {
|
|
159
159
|
const r = {};
|
|
160
160
|
for (const [code, name] of x) {
|
|
161
|
-
r[
|
|
162
|
-
r[
|
|
161
|
+
r[`is${name}`] = (flags) => !!(flags & code);
|
|
162
|
+
r[`set${name}`] = (flags) => flags | code;
|
|
163
163
|
}
|
|
164
164
|
return r;
|
|
165
165
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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