@gmod/cram 1.6.3 → 1.7.0
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/CHANGELOG.md +9 -0
- package/dist/craiIndex.d.ts +19 -12
- package/dist/craiIndex.js +63 -123
- package/dist/craiIndex.js.map +1 -1
- package/dist/cram-bundle.js +2 -17
- package/dist/cram-bundle.js.LICENSE.txt +17 -0
- package/dist/cramFile/codecs/_base.d.ts +26 -5
- package/dist/cramFile/codecs/_base.js +3 -39
- package/dist/cramFile/codecs/_base.js.map +1 -1
- package/dist/cramFile/codecs/beta.d.ts +7 -3
- package/dist/cramFile/codecs/beta.js +13 -31
- package/dist/cramFile/codecs/beta.js.map +1 -1
- package/dist/cramFile/codecs/byteArrayLength.d.ts +13 -7
- package/dist/cramFile/codecs/byteArrayLength.js +22 -41
- package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
- package/dist/cramFile/codecs/byteArrayStop.d.ts +9 -5
- package/dist/cramFile/codecs/byteArrayStop.js +25 -46
- package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
- package/dist/cramFile/codecs/dataSeriesTypes.d.ts +4 -0
- package/dist/cramFile/codecs/dataSeriesTypes.js +3 -0
- package/dist/cramFile/codecs/dataSeriesTypes.js.map +1 -0
- package/dist/cramFile/codecs/external.d.ts +10 -6
- package/dist/cramFile/codecs/external.js +26 -44
- package/dist/cramFile/codecs/external.js.map +1 -1
- package/dist/cramFile/codecs/gamma.d.ts +7 -3
- package/dist/cramFile/codecs/gamma.js +16 -34
- package/dist/cramFile/codecs/gamma.js.map +1 -1
- package/dist/cramFile/codecs/getBits.d.ts +7 -0
- package/dist/cramFile/codecs/getBits.js +26 -0
- package/dist/cramFile/codecs/getBits.js.map +1 -0
- package/dist/cramFile/codecs/huffman.d.ts +17 -13
- package/dist/cramFile/codecs/huffman.js +76 -85
- package/dist/cramFile/codecs/huffman.js.map +1 -1
- package/dist/cramFile/codecs/index.d.ts +4 -2
- package/dist/cramFile/codecs/index.js +12 -13
- package/dist/cramFile/codecs/index.js.map +1 -1
- package/dist/cramFile/codecs/subexp.d.ts +7 -3
- package/dist/cramFile/codecs/subexp.js +19 -36
- package/dist/cramFile/codecs/subexp.js.map +1 -1
- package/dist/cramFile/constants.d.ts +35 -35
- package/dist/cramFile/constants.js +1 -1
- package/dist/cramFile/constants.js.map +1 -1
- package/dist/cramFile/container/compressionScheme.d.ts +57 -11
- package/dist/cramFile/container/compressionScheme.js +37 -32
- package/dist/cramFile/container/compressionScheme.js.map +1 -1
- package/dist/cramFile/container/index.d.ts +23 -9
- package/dist/cramFile/container/index.js +74 -144
- package/dist/cramFile/container/index.js.map +1 -1
- package/dist/cramFile/encoding.d.ts +78 -0
- package/dist/cramFile/encoding.js +3 -0
- package/dist/cramFile/encoding.js.map +1 -0
- package/dist/cramFile/file.d.ts +91 -41
- package/dist/cramFile/file.js +234 -368
- package/dist/cramFile/file.js.map +1 -1
- package/dist/cramFile/filehandle.d.ts +2 -0
- package/dist/cramFile/filehandle.js +3 -0
- package/dist/cramFile/filehandle.js.map +1 -0
- package/dist/cramFile/index.d.ts +1 -1
- package/dist/cramFile/index.js +1 -1
- package/dist/cramFile/index.js.map +1 -1
- package/dist/cramFile/record.d.ts +61 -17
- package/dist/cramFile/record.js +153 -77
- package/dist/cramFile/record.js.map +1 -1
- package/dist/cramFile/sectionParsers.d.ts +99 -8
- package/dist/cramFile/sectionParsers.js +70 -80
- package/dist/cramFile/sectionParsers.js.map +1 -1
- package/dist/cramFile/slice/decodeRecord.d.ts +30 -2
- package/dist/cramFile/slice/decodeRecord.js +148 -118
- package/dist/cramFile/slice/decodeRecord.js.map +1 -1
- package/dist/cramFile/slice/index.d.ts +21 -14
- package/dist/cramFile/slice/index.js +286 -381
- package/dist/cramFile/slice/index.js.map +1 -1
- package/dist/cramFile/util.d.ts +11 -5
- package/dist/cramFile/util.js +19 -97
- package/dist/cramFile/util.js.map +1 -1
- package/dist/errors.d.ts +5 -10
- package/dist/errors.js +11 -62
- package/dist/errors.js.map +1 -1
- package/dist/index.d.ts +3 -3
- package/dist/index.js +3 -3
- package/dist/index.js.map +1 -1
- package/dist/indexedCramFile.d.ts +37 -12
- package/dist/indexedCramFile.js +114 -154
- package/dist/indexedCramFile.js.map +1 -1
- package/dist/io/index.d.ts +5 -5
- package/dist/io/index.js +9 -9
- package/dist/io/index.js.map +1 -1
- package/dist/rans/constants.js +3 -3
- package/dist/rans/constants.js.map +1 -1
- package/dist/rans/d04.js +15 -15
- package/dist/rans/d04.js.map +1 -1
- package/dist/rans/d14.js +21 -21
- package/dist/rans/d14.js.map +1 -1
- package/dist/rans/decoding.js +27 -30
- package/dist/rans/decoding.js.map +1 -1
- package/dist/rans/frequencies.js +11 -11
- package/dist/rans/frequencies.js.map +1 -1
- package/dist/rans/index.js +46 -49
- package/dist/rans/index.js.map +1 -1
- package/dist/sam.d.ts +8 -1
- package/dist/sam.js +7 -7
- package/dist/sam.js.map +1 -1
- package/dist/typescript.d.ts +3 -0
- package/dist/typescript.js +11 -0
- package/dist/typescript.js.map +1 -0
- package/dist/unzip-pako.js +1 -1
- package/dist/unzip-pako.js.map +1 -1
- package/dist/unzip.js +1 -1
- package/dist/unzip.js.map +1 -1
- package/errors.js +11 -62
- package/esm/craiIndex.d.ts +19 -12
- package/esm/craiIndex.js +8 -24
- package/esm/craiIndex.js.map +1 -1
- package/esm/cramFile/codecs/_base.d.ts +26 -5
- package/esm/cramFile/codecs/_base.js +1 -35
- package/esm/cramFile/codecs/_base.js.map +1 -1
- package/esm/cramFile/codecs/beta.d.ts +7 -3
- package/esm/cramFile/codecs/beta.js +4 -3
- package/esm/cramFile/codecs/beta.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayLength.d.ts +13 -7
- package/esm/cramFile/codecs/byteArrayLength.js +1 -1
- package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayStop.d.ts +9 -5
- package/esm/cramFile/codecs/byteArrayStop.js +7 -9
- package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
- package/esm/cramFile/codecs/dataSeriesTypes.d.ts +4 -0
- package/esm/cramFile/codecs/dataSeriesTypes.js +2 -0
- package/esm/cramFile/codecs/dataSeriesTypes.js.map +1 -0
- package/esm/cramFile/codecs/external.d.ts +10 -6
- package/esm/cramFile/codecs/external.js +4 -3
- package/esm/cramFile/codecs/external.js.map +1 -1
- package/esm/cramFile/codecs/gamma.d.ts +7 -3
- package/esm/cramFile/codecs/gamma.js +5 -4
- package/esm/cramFile/codecs/gamma.js.map +1 -1
- package/esm/cramFile/codecs/getBits.d.ts +7 -0
- package/esm/cramFile/codecs/getBits.js +21 -0
- package/esm/cramFile/codecs/getBits.js.map +1 -0
- package/esm/cramFile/codecs/huffman.d.ts +17 -13
- package/esm/cramFile/codecs/huffman.js +22 -9
- package/esm/cramFile/codecs/huffman.js.map +1 -1
- package/esm/cramFile/codecs/index.d.ts +4 -2
- package/esm/cramFile/codecs/index.js +1 -1
- package/esm/cramFile/codecs/index.js.map +1 -1
- package/esm/cramFile/codecs/subexp.d.ts +7 -3
- package/esm/cramFile/codecs/subexp.js +7 -5
- package/esm/cramFile/codecs/subexp.js.map +1 -1
- package/esm/cramFile/constants.d.ts +35 -35
- package/esm/cramFile/constants.js.map +1 -1
- package/esm/cramFile/container/compressionScheme.d.ts +57 -11
- package/esm/cramFile/container/compressionScheme.js +15 -8
- package/esm/cramFile/container/compressionScheme.js.map +1 -1
- package/esm/cramFile/container/index.d.ts +23 -9
- package/esm/cramFile/container/index.js +11 -9
- package/esm/cramFile/container/index.js.map +1 -1
- package/esm/cramFile/encoding.d.ts +78 -0
- package/esm/cramFile/encoding.js +2 -0
- package/esm/cramFile/encoding.js.map +1 -0
- package/esm/cramFile/file.d.ts +91 -41
- package/esm/cramFile/file.js +59 -47
- package/esm/cramFile/file.js.map +1 -1
- package/esm/cramFile/filehandle.d.ts +2 -0
- package/esm/cramFile/filehandle.js +2 -0
- package/esm/cramFile/filehandle.js.map +1 -0
- package/esm/cramFile/index.d.ts +1 -1
- package/esm/cramFile/index.js.map +1 -1
- package/esm/cramFile/record.d.ts +61 -17
- package/esm/cramFile/record.js +83 -5
- package/esm/cramFile/record.js.map +1 -1
- package/esm/cramFile/sectionParsers.d.ts +99 -8
- package/esm/cramFile/sectionParsers.js +7 -17
- package/esm/cramFile/sectionParsers.js.map +1 -1
- package/esm/cramFile/slice/decodeRecord.d.ts +30 -2
- package/esm/cramFile/slice/decodeRecord.js +102 -70
- package/esm/cramFile/slice/decodeRecord.js.map +1 -1
- package/esm/cramFile/slice/index.d.ts +21 -14
- package/esm/cramFile/slice/index.js +77 -38
- package/esm/cramFile/slice/index.js.map +1 -1
- package/esm/cramFile/util.d.ts +11 -5
- package/esm/cramFile/util.js +11 -82
- package/esm/cramFile/util.js.map +1 -1
- package/esm/errors.d.ts +5 -10
- package/esm/errors.js +0 -5
- package/esm/errors.js.map +1 -1
- package/esm/index.d.ts +3 -3
- package/esm/index.js.map +1 -1
- package/esm/indexedCramFile.d.ts +37 -12
- package/esm/indexedCramFile.js +19 -8
- package/esm/indexedCramFile.js.map +1 -1
- package/esm/io/index.d.ts +5 -5
- package/esm/io/index.js +3 -3
- package/esm/io/index.js.map +1 -1
- package/esm/sam.d.ts +8 -1
- package/esm/sam.js.map +1 -1
- package/esm/typescript.d.ts +3 -0
- package/esm/typescript.js +7 -0
- package/esm/typescript.js.map +1 -0
- package/package.json +18 -11
- package/src/{craiIndex.js → craiIndex.ts} +37 -31
- package/src/cramFile/codecs/_base.ts +45 -0
- package/src/cramFile/codecs/beta.ts +34 -0
- package/src/cramFile/codecs/{byteArrayLength.js → byteArrayLength.ts} +27 -5
- package/src/cramFile/codecs/{byteArrayStop.js → byteArrayStop.ts} +25 -12
- package/src/cramFile/codecs/dataSeriesTypes.ts +39 -0
- package/src/cramFile/codecs/{external.js → external.ts} +28 -12
- package/src/cramFile/codecs/gamma.ts +42 -0
- package/src/cramFile/codecs/getBits.ts +28 -0
- package/src/cramFile/codecs/{huffman.js → huffman.ts} +48 -15
- package/src/cramFile/codecs/{index.js → index.ts} +9 -3
- package/src/cramFile/codecs/subexp.ts +45 -0
- package/src/cramFile/{constants.js → constants.ts} +0 -0
- package/src/cramFile/container/{compressionScheme.js → compressionScheme.ts} +50 -18
- package/src/cramFile/container/{index.js → index.ts} +13 -13
- package/src/cramFile/encoding.ts +98 -0
- package/src/cramFile/{file.js → file.ts} +136 -62
- package/src/cramFile/filehandle.ts +3 -0
- package/src/cramFile/{index.js → index.ts} +0 -0
- package/src/cramFile/{record.js → record.ts} +185 -14
- package/src/cramFile/{sectionParsers.js → sectionParsers.ts} +148 -20
- package/src/cramFile/slice/{decodeRecord.js → decodeRecord.ts} +158 -105
- package/src/cramFile/slice/{index.js → index.ts} +138 -63
- package/src/cramFile/{util.js → util.ts} +28 -17
- package/src/{errors.js → errors.ts} +0 -5
- package/src/{index.js → index.ts} +0 -0
- package/src/{indexedCramFile.js → indexedCramFile.ts} +79 -19
- package/src/io/{index.js → index.ts} +10 -5
- package/src/{sam.js → sam.ts} +7 -2
- package/src/typescript.ts +17 -0
- package/src/typings/binary-parser.d.ts +44 -0
- package/src/typings/bzip2.d.ts +7 -0
- package/src/typings/htscodecs.d.ts +6 -0
- package/dist/io/bufferCache.d.ts +0 -12
- package/dist/io/bufferCache.js +0 -112
- package/dist/io/bufferCache.js.map +0 -1
- package/dist/io/localFile.d.ts +0 -10
- package/dist/io/localFile.js +0 -108
- package/dist/io/localFile.js.map +0 -1
- package/dist/io/remoteFile.d.ts +0 -16
- package/dist/io/remoteFile.js +0 -143
- package/dist/io/remoteFile.js.map +0 -1
- package/esm/io/bufferCache.d.ts +0 -12
- package/esm/io/bufferCache.js +0 -54
- package/esm/io/bufferCache.js.map +0 -1
- package/esm/io/localFile.d.ts +0 -10
- package/esm/io/localFile.js +0 -31
- package/esm/io/localFile.js.map +0 -1
- package/esm/io/remoteFile.d.ts +0 -16
- package/esm/io/remoteFile.js +0 -64
- package/esm/io/remoteFile.js.map +0 -1
- package/src/cramFile/codecs/_base.js +0 -49
- package/src/cramFile/codecs/beta.js +0 -23
- package/src/cramFile/codecs/gamma.js +0 -30
- package/src/cramFile/codecs/subexp.js +0 -32
- package/src/io/bufferCache.js +0 -66
- package/src/io/localFile.js +0 -35
- package/src/io/remoteFile.js +0 -71
package/dist/rans/decoding.js
CHANGED
|
@@ -1,43 +1,40 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
|
|
4
|
-
|
|
5
|
-
|
|
3
|
+
const errors_1 = require("../errors");
|
|
4
|
+
const constants_1 = require("./constants");
|
|
5
|
+
class FC {
|
|
6
6
|
// int F, C;
|
|
7
|
-
|
|
7
|
+
constructor() {
|
|
8
8
|
this.F = undefined;
|
|
9
9
|
this.C = undefined;
|
|
10
10
|
}
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
var AriDecoder = /** @class */ (function () {
|
|
11
|
+
}
|
|
12
|
+
class AriDecoder {
|
|
14
13
|
// final FC[] fc = new FC[256];
|
|
15
14
|
// byte[] R;
|
|
16
|
-
|
|
15
|
+
constructor() {
|
|
17
16
|
this.fc = new Array(256);
|
|
18
|
-
for (
|
|
17
|
+
for (let i = 0; i < this.fc.length; i += 1) {
|
|
19
18
|
this.fc[i] = new FC();
|
|
20
19
|
}
|
|
21
20
|
this.R = null;
|
|
22
21
|
}
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
var Symbol = /** @class */ (function () {
|
|
22
|
+
}
|
|
23
|
+
class Symbol {
|
|
26
24
|
// int start; // Start of range.
|
|
27
25
|
// int freq; // Symbol frequency.
|
|
28
|
-
|
|
26
|
+
constructor() {
|
|
29
27
|
this.start = undefined;
|
|
30
28
|
this.freq = undefined;
|
|
31
29
|
}
|
|
32
|
-
|
|
33
|
-
}());
|
|
30
|
+
}
|
|
34
31
|
// Initialize a decoder symbol to start "start" and frequency "freq"
|
|
35
32
|
function symbolInit(sym, start, freq) {
|
|
36
33
|
if (!(start <= 1 << 16)) {
|
|
37
|
-
throw new errors_1.CramMalformedError(
|
|
34
|
+
throw new errors_1.CramMalformedError(`assertion failed: start <= 1<<16`);
|
|
38
35
|
}
|
|
39
36
|
if (!(freq <= (1 << 16) - start)) {
|
|
40
|
-
throw new errors_1.CramMalformedError(
|
|
37
|
+
throw new errors_1.CramMalformedError(`assertion failed: freq <= 1<<16`);
|
|
41
38
|
}
|
|
42
39
|
sym.start = start;
|
|
43
40
|
sym.freq = freq;
|
|
@@ -51,7 +48,7 @@ function symbolInit(sym, start, freq) {
|
|
|
51
48
|
/* final int */ start,
|
|
52
49
|
/* final int */ freq,
|
|
53
50
|
/* final int */ scaleBits) {
|
|
54
|
-
/* final int */
|
|
51
|
+
/* final int */ const mask = (1 << scaleBits) - 1;
|
|
55
52
|
// s, x = D(x)
|
|
56
53
|
return freq * (r >> scaleBits) + (r & mask) - start;
|
|
57
54
|
}
|
|
@@ -76,13 +73,13 @@ function symbolInit(sym, start, freq) {
|
|
|
76
73
|
/* final int */ start,
|
|
77
74
|
/* final int */ freq,
|
|
78
75
|
/* final int */ scaleBits) {
|
|
79
|
-
/* final int */
|
|
76
|
+
/* final int */ const mask = (1 << scaleBits) - 1;
|
|
80
77
|
// s, x = D(x)
|
|
81
78
|
r = freq * (r >> scaleBits) + (r & mask) - start;
|
|
82
79
|
// re-normalize
|
|
83
80
|
if (r < constants_1.RANS_BYTE_L) {
|
|
84
81
|
do {
|
|
85
|
-
/* final int */
|
|
82
|
+
/* final int */ const b = 0xff & pptr.get();
|
|
86
83
|
r = (r << 8) | b;
|
|
87
84
|
} while (r < constants_1.RANS_BYTE_L);
|
|
88
85
|
}
|
|
@@ -108,16 +105,16 @@ function symbolInit(sym, start, freq) {
|
|
|
108
105
|
}
|
|
109
106
|
return r;
|
|
110
107
|
}
|
|
111
|
-
|
|
112
|
-
FC
|
|
113
|
-
AriDecoder
|
|
114
|
-
Symbol
|
|
115
|
-
symbolInit
|
|
116
|
-
advanceStep
|
|
117
|
-
advanceSymbolStep
|
|
118
|
-
get
|
|
119
|
-
advanceSymbol
|
|
120
|
-
renormalize
|
|
108
|
+
const Decode = {
|
|
109
|
+
FC,
|
|
110
|
+
AriDecoder,
|
|
111
|
+
Symbol,
|
|
112
|
+
symbolInit,
|
|
113
|
+
advanceStep,
|
|
114
|
+
advanceSymbolStep,
|
|
115
|
+
get,
|
|
116
|
+
advanceSymbol,
|
|
117
|
+
renormalize,
|
|
121
118
|
};
|
|
122
119
|
exports.default = Decode;
|
|
123
120
|
//# sourceMappingURL=decoding.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"decoding.js","sourceRoot":"","sources":["../../src/rans/decoding.js"],"names":[],"mappings":";;AAAA,
|
|
1
|
+
{"version":3,"file":"decoding.js","sourceRoot":"","sources":["../../src/rans/decoding.js"],"names":[],"mappings":";;AAAA,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;YAC1C,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,EAAE,EAAE,CAAA;SACtB;QACD,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;IACf,CAAC;CACF;AAED,MAAM,MAAM;IACV,gCAAgC;IAChC,iCAAiC;IACjC;QACE,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;QACtB,IAAI,CAAC,IAAI,GAAG,SAAS,CAAA;IACvB,CAAC;CACF;AAED,oEAAoE;AACpE,SAAS,UAAU,CAAC,GAAG,EAAE,KAAK,EAAE,IAAI;IAClC,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,IAAI,EAAE,CAAC,EAAE;QACvB,MAAM,IAAI,2BAAkB,CAAC,kCAAkC,CAAC,CAAA;KACjE;IACD,IAAI,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,KAAK,CAAC,EAAE;QAChC,MAAM,IAAI,2BAAkB,CAAC,iCAAiC,CAAC,CAAA;KAChE;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;QACnB,GAAG;YACD,eAAe,CAAC,MAAM,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,GAAG,EAAE,CAAA;YAC3C,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;SACjB,QAAQ,CAAC,GAAG,uBAAW,EAAC;KAC1B;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;QACnB,GAAG;YACD,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,CAAA;SACnC,QAAQ,CAAC,GAAG,uBAAW,EAAC;KAC1B;IAED,OAAO,CAAC,CAAA;AACV,CAAC;AAED,MAAM,MAAM,GAAG;IACb,EAAE;IACF,UAAU;IACV,MAAM;IACN,UAAU;IACV,WAAW;IACX,iBAAiB;IACjB,GAAG;IACH,aAAa;IACb,WAAW;CACZ,CAAA;AAED,kBAAe,MAAM,CAAA"}
|
package/dist/rans/frequencies.js
CHANGED
|
@@ -4,9 +4,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
exports.readStatsO1 = exports.readStatsO0 = void 0;
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
7
|
+
const errors_1 = require("../errors");
|
|
8
|
+
const constants_1 = require("./constants");
|
|
9
|
+
const decoding_1 = __importDefault(require("./decoding"));
|
|
10
10
|
function assert(result) {
|
|
11
11
|
if (!result) {
|
|
12
12
|
throw new errors_1.CramMalformedError('assertion failed');
|
|
@@ -17,9 +17,9 @@ function readStatsO0(
|
|
|
17
17
|
/* Decoding.AriDecoder */ decoder,
|
|
18
18
|
/* Decoding.RansDecSymbol[] */ syms) {
|
|
19
19
|
// Pre-compute reverse lookup of frequency.
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
|
|
20
|
+
let rle = 0;
|
|
21
|
+
let x = 0;
|
|
22
|
+
let j = cp.get() & 0xff;
|
|
23
23
|
do {
|
|
24
24
|
if (decoder.fc[j] == null) {
|
|
25
25
|
decoder.fc[j] = new decoding_1.default.FC();
|
|
@@ -56,12 +56,12 @@ function readStatsO1(
|
|
|
56
56
|
/* ByteBuffer */ cp,
|
|
57
57
|
/* Decoding.AriDecoder[] */ D,
|
|
58
58
|
/* Decoding.RansDecSymbol[][] */ syms) {
|
|
59
|
-
|
|
60
|
-
|
|
59
|
+
let rlei = 0;
|
|
60
|
+
let i = 0xff & cp.get();
|
|
61
61
|
do {
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
|
|
62
|
+
let rlej = 0;
|
|
63
|
+
let x = 0;
|
|
64
|
+
let j = 0xff & cp.get();
|
|
65
65
|
if (D[i] == null) {
|
|
66
66
|
D[i] = new decoding_1.default.AriDecoder();
|
|
67
67
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"frequencies.js","sourceRoot":"","sources":["../../src/rans/frequencies.js"],"names":[],"mappings":";;;;;;AAAA,
|
|
1
|
+
{"version":3,"file":"frequencies.js","sourceRoot":"","sources":["../../src/rans/frequencies.js"],"names":[],"mappings":";;;;;;AAAA,sCAA8C;AAE9C,2CAAqC;AACrC,0DAAiC;AAEjC,SAAS,MAAM,CAAC,MAAM;IACpB,IAAI,CAAC,MAAM,EAAE;QACX,MAAM,IAAI,2BAAkB,CAAC,kBAAkB,CAAC,CAAA;KACjD;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;QACD,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;YACzB,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,EAAE,EAAE,CAAA;SAClC;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;YAC1B,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;SACrE;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;YACd,OAAO,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,mBAAO,CAAC,CAAA;SAC/B;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;YAC/D,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;YACnB,GAAG,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;SACtB;aAAM,IAAI,GAAG,KAAK,CAAC,EAAE;YACpB,GAAG,IAAI,CAAC,CAAA;YACR,CAAC,IAAI,CAAC,CAAA;SACP;aAAM;YACL,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;SACpB;KACF,QAAQ,CAAC,KAAK,CAAC,EAAC;IAEjB,MAAM,CAAC,CAAC,GAAG,mBAAO,CAAC,CAAA;AACrB,CAAC;AA1CD,kCA0CC;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;QACD,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;YAChB,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,UAAU,EAAE,CAAA;SACjC;QACD,GAAG;YACD,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;gBACtB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,EAAE,EAAE,CAAA;aAC/B;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;gBACvB,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;aAC/D;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;gBACtB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,mBAAO,CAAA;aACvB;YAED,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;gBACtB,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,aAAa,EAAE,CAAA;aAC1C;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;gBAClB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,mBAAO,CAAC,CAAA;aAC5B;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;gBAChE,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;gBACnB,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;aACvB;iBAAM,IAAI,IAAI,KAAK,CAAC,EAAE;gBACrB,IAAI,IAAI,CAAC,CAAA;gBACT,CAAC,IAAI,CAAC,CAAA;aACP;iBAAM;gBACL,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;aACpB;SACF,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;YAChE,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YACnB,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;SACvB;aAAM,IAAI,IAAI,KAAK,CAAC,EAAE;YACrB,IAAI,IAAI,CAAC,CAAA;YACT,CAAC,IAAI,CAAC,CAAA;SACP;aAAM;YACL,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;SACpB;KACF,QAAQ,CAAC,KAAK,CAAC,EAAC;AACnB,CAAC;AAjED,kCAiEC"}
|
package/dist/rans/index.js
CHANGED
|
@@ -3,14 +3,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
-
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
6
|
+
const errors_1 = require("../errors");
|
|
7
|
+
const decoding_1 = __importDefault(require("./decoding"));
|
|
8
|
+
const frequencies_1 = require("./frequencies");
|
|
9
|
+
const d04_1 = __importDefault(require("./d04"));
|
|
10
|
+
const d14_1 = __importDefault(require("./d14"));
|
|
11
11
|
// const /* int */ ORDER_BYTE_LENGTH = 1
|
|
12
12
|
// const /* int */ COMPRESSED_BYTE_LENGTH = 4
|
|
13
|
-
|
|
13
|
+
const /* int */ RAW_BYTE_LENGTH = 4;
|
|
14
14
|
// const /* int */ PREFIX_BYTE_LENGTH =
|
|
15
15
|
// ORDER_BYTE_LENGTH + COMPRESSED_BYTE_LENGTH + RAW_BYTE_LENGTH
|
|
16
16
|
// enum ORDER {
|
|
@@ -96,9 +96,9 @@ function uncompressOrder0Way4(
|
|
|
96
96
|
/* const ByteBuffer */ input,
|
|
97
97
|
/* const ByteBuffer */ out) {
|
|
98
98
|
// input.order(ByteOrder.LITTLE_ENDIAN);
|
|
99
|
-
|
|
100
|
-
|
|
101
|
-
for (
|
|
99
|
+
const D = new decoding_1.default.AriDecoder();
|
|
100
|
+
const syms = new Array(256);
|
|
101
|
+
for (let i = 0; i < syms.length; i += 1) {
|
|
102
102
|
syms[i] = new decoding_1.default.Symbol();
|
|
103
103
|
}
|
|
104
104
|
(0, frequencies_1.readStatsO0)(input, D, syms);
|
|
@@ -108,14 +108,14 @@ function uncompressOrder0Way4(
|
|
|
108
108
|
function uncompressOrder1Way4(
|
|
109
109
|
/* const ByteBuffer */ input,
|
|
110
110
|
/* const ByteBuffer */ output) {
|
|
111
|
-
|
|
112
|
-
for (
|
|
111
|
+
const D = new Array(256);
|
|
112
|
+
for (let i = 0; i < D.length; i += 1) {
|
|
113
113
|
D[i] = new decoding_1.default.AriDecoder();
|
|
114
114
|
}
|
|
115
|
-
|
|
116
|
-
for (
|
|
115
|
+
const /* Decoding.RansDecSymbol[][] */ syms = new Array(256);
|
|
116
|
+
for (let i = 0; i < syms.length; i += 1) {
|
|
117
117
|
syms[i] = new Array(256);
|
|
118
|
-
for (
|
|
118
|
+
for (let j = 0; j < syms[i].length; j += 1) {
|
|
119
119
|
syms[i][j] = new decoding_1.default.Symbol();
|
|
120
120
|
}
|
|
121
121
|
}
|
|
@@ -124,72 +124,69 @@ function uncompressOrder1Way4(
|
|
|
124
124
|
return output;
|
|
125
125
|
}
|
|
126
126
|
/* compat layer to make a node buffer act like a java ByteBuffer */
|
|
127
|
-
|
|
128
|
-
|
|
129
|
-
if (initialInputPosition === void 0) { initialInputPosition = 0; }
|
|
127
|
+
class ByteBuffer {
|
|
128
|
+
constructor(nodeBuffer, initialInputPosition = 0) {
|
|
130
129
|
this._buffer = nodeBuffer;
|
|
131
130
|
this._position = initialInputPosition;
|
|
132
131
|
this.length = nodeBuffer.length;
|
|
133
132
|
}
|
|
134
|
-
|
|
135
|
-
|
|
133
|
+
get() {
|
|
134
|
+
const b = this._buffer[this._position];
|
|
136
135
|
this._position += 1;
|
|
137
136
|
return b;
|
|
138
|
-
}
|
|
139
|
-
|
|
137
|
+
}
|
|
138
|
+
getByte() {
|
|
140
139
|
return this.get();
|
|
141
|
-
}
|
|
142
|
-
|
|
140
|
+
}
|
|
141
|
+
getByteAt(position) {
|
|
143
142
|
return this._buffer[position];
|
|
144
|
-
}
|
|
145
|
-
|
|
143
|
+
}
|
|
144
|
+
position() {
|
|
146
145
|
return this._position;
|
|
147
|
-
}
|
|
148
|
-
|
|
146
|
+
}
|
|
147
|
+
put(val) {
|
|
149
148
|
this._buffer[this._position] = val;
|
|
150
149
|
this._position += 1;
|
|
151
150
|
return val;
|
|
152
|
-
}
|
|
153
|
-
|
|
151
|
+
}
|
|
152
|
+
putAt(position, val) {
|
|
154
153
|
this._buffer[position] = val;
|
|
155
154
|
return val;
|
|
156
|
-
}
|
|
157
|
-
|
|
155
|
+
}
|
|
156
|
+
setPosition(pos) {
|
|
158
157
|
this._position = pos;
|
|
159
158
|
return pos;
|
|
160
|
-
}
|
|
161
|
-
|
|
162
|
-
|
|
159
|
+
}
|
|
160
|
+
getInt() {
|
|
161
|
+
const i = this._buffer.readInt32LE(this._position);
|
|
163
162
|
this._position += 4;
|
|
164
163
|
return i;
|
|
165
|
-
}
|
|
166
|
-
|
|
164
|
+
}
|
|
165
|
+
remaining() {
|
|
167
166
|
return this._buffer.length - this._position;
|
|
168
|
-
}
|
|
169
|
-
|
|
170
|
-
}());
|
|
167
|
+
}
|
|
168
|
+
}
|
|
171
169
|
// static /* const */ ByteBuffer EMPTY_BUFFER = ByteBuffer.allocate(0);
|
|
172
|
-
function uncompress(inputBuffer, outputBuffer, initialInputPosition) {
|
|
173
|
-
if (initialInputPosition === void 0) { initialInputPosition = 0; }
|
|
170
|
+
function uncompress(inputBuffer, outputBuffer, initialInputPosition = 0) {
|
|
174
171
|
if (inputBuffer.length === 0) {
|
|
175
172
|
outputBuffer.fill(0);
|
|
176
173
|
return outputBuffer;
|
|
177
174
|
}
|
|
178
|
-
|
|
175
|
+
const input = new ByteBuffer(inputBuffer, initialInputPosition);
|
|
179
176
|
// input.order(ByteOrder.LITTLE_ENDIAN);
|
|
180
|
-
|
|
177
|
+
const order = input.get();
|
|
181
178
|
if (order !== 0 && order !== 1) {
|
|
182
|
-
throw new errors_1.CramMalformedError(
|
|
179
|
+
throw new errors_1.CramMalformedError(`Invalid rANS order ${order}`);
|
|
183
180
|
}
|
|
184
|
-
|
|
181
|
+
const /* int */ inputSize = input.getInt();
|
|
185
182
|
if (inputSize !== input.remaining() - RAW_BYTE_LENGTH) {
|
|
186
183
|
throw new errors_1.CramMalformedError('Incorrect input length.');
|
|
187
184
|
}
|
|
188
|
-
|
|
189
|
-
|
|
185
|
+
const /* int */ outputSize = input.getInt();
|
|
186
|
+
const output = new ByteBuffer(outputBuffer || Buffer.allocUnsafe(outputSize));
|
|
190
187
|
// TODO output.limit(outputSize)
|
|
191
188
|
if (output.length < outputSize) {
|
|
192
|
-
throw new errors_1.CramMalformedError(
|
|
189
|
+
throw new errors_1.CramMalformedError(`Output buffer too small to fit ${outputSize} bytes.`);
|
|
193
190
|
}
|
|
194
191
|
switch (order) {
|
|
195
192
|
case 0:
|
|
@@ -197,7 +194,7 @@ function uncompress(inputBuffer, outputBuffer, initialInputPosition) {
|
|
|
197
194
|
case 1:
|
|
198
195
|
return uncompressOrder1Way4(input, output);
|
|
199
196
|
default:
|
|
200
|
-
throw new errors_1.CramMalformedError(
|
|
197
|
+
throw new errors_1.CramMalformedError(`Invalid rANS order: ${order}`);
|
|
201
198
|
}
|
|
202
199
|
}
|
|
203
200
|
exports.default = uncompress;
|
package/dist/rans/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/rans/index.js"],"names":[],"mappings":";;;;;AAAA,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/rans/index.js"],"names":[],"mappings":";;;;;AAAA,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;QACvC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,MAAM,EAAE,CAAA;KAChC;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;QACpC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,UAAU,EAAE,CAAA;KACjC;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;QACvC,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;YAC1C,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,MAAM,EAAE,CAAA;SACnC;KACF;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;QAC5B,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACpB,OAAO,YAAY,CAAA;KACpB;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;QAC9B,MAAM,IAAI,2BAAkB,CAAC,sBAAsB,KAAK,EAAE,CAAC,CAAA;KAC5D;IAED,MAAM,SAAS,CAAC,SAAS,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1C,IAAI,SAAS,KAAK,KAAK,CAAC,SAAS,EAAE,GAAG,eAAe,EAAE;QACrD,MAAM,IAAI,2BAAkB,CAAC,yBAAyB,CAAC,CAAA;KACxD;IAED,MAAM,SAAS,CAAC,UAAU,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC3C,MAAM,MAAM,GAAG,IAAI,UAAU,CAAC,YAAY,IAAI,MAAM,CAAC,WAAW,CAAC,UAAU,CAAC,CAAC,CAAA;IAC7E,gCAAgC;IAEhC,IAAI,MAAM,CAAC,MAAM,GAAG,UAAU,EAAE;QAC9B,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,UAAU,SAAS,CACtD,CAAA;KACF;IAED,QAAQ,KAAK,EAAE;QACb,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;KAC/D;AACH,CAAC;AA3CD,6BA2CC"}
|
package/dist/sam.d.ts
CHANGED
package/dist/sam.js
CHANGED
|
@@ -2,13 +2,13 @@
|
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
exports.parseHeaderText = void 0;
|
|
4
4
|
function parseHeaderText(text) {
|
|
5
|
-
|
|
6
|
-
|
|
7
|
-
lines.forEach(
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
return { tag: fieldTag, value
|
|
5
|
+
const lines = text.split(/\r?\n/);
|
|
6
|
+
const data = [];
|
|
7
|
+
lines.forEach(line => {
|
|
8
|
+
const [tag, ...fields] = line.split(/\t/);
|
|
9
|
+
const parsedFields = fields.map(f => {
|
|
10
|
+
const [fieldTag, value] = f.split(':', 2);
|
|
11
|
+
return { tag: fieldTag, value };
|
|
12
12
|
});
|
|
13
13
|
if (tag) {
|
|
14
14
|
data.push({ tag: tag.substr(1), data: parsedFields });
|
package/dist/sam.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.
|
|
1
|
+
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;;AAKA,SAAgB,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAAqB,EAAE,CAAA;IACjC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;QACnB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,MAAM,YAAY,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YAClC,MAAM,CAAC,QAAQ,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YACzC,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QACjC,CAAC,CAAC,CAAA;QACF,IAAI,GAAG,EAAE;YACP,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,CAAA;SACtD;IACH,CAAC,CAAC,CAAA;IACF,OAAO,IAAI,CAAA;AACb,CAAC;AAdD,0CAcC"}
|
|
@@ -0,0 +1,3 @@
|
|
|
1
|
+
export declare function ensureNotNullish<T>(x: T | null | undefined): T;
|
|
2
|
+
export declare type TupleOf<T, N extends number> = N extends N ? number extends N ? T[] : _TupleOf<T, N, []> : never;
|
|
3
|
+
export declare type _TupleOf<T, N extends number, R extends unknown[]> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>;
|
|
@@ -0,0 +1,11 @@
|
|
|
1
|
+
"use strict";
|
|
2
|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
+
exports.ensureNotNullish = void 0;
|
|
4
|
+
function ensureNotNullish(x) {
|
|
5
|
+
if (x === null || x === undefined) {
|
|
6
|
+
throw new Error('Value must not be nullish.');
|
|
7
|
+
}
|
|
8
|
+
return x;
|
|
9
|
+
}
|
|
10
|
+
exports.ensureNotNullish = ensureNotNullish;
|
|
11
|
+
//# sourceMappingURL=typescript.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":";;;AAAA,SAAgB,gBAAgB,CAAI,CAAuB;IACzD,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,SAAS,EAAE;QACjC,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;KAC9C;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AALD,4CAKC"}
|
package/dist/unzip-pako.js
CHANGED
package/dist/unzip-pako.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;;AAAA
|
|
1
|
+
{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;;AAAA,+BAA8B;AAE9B,SAAgB,KAAK,CAAC,KAAa;IACjC,OAAO,MAAM,CAAC,IAAI,CAAC,IAAA,cAAO,EAAC,KAAK,CAAC,CAAC,CAAA;AACpC,CAAC;AAFD,sBAEC"}
|
package/dist/unzip.js
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
exports.unzip = void 0;
|
|
4
|
-
|
|
4
|
+
const zlib_1 = require("zlib");
|
|
5
5
|
Object.defineProperty(exports, "unzip", { enumerable: true, get: function () { return zlib_1.gunzipSync; } });
|
|
6
6
|
//# 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":";;;AAAA
|
|
1
|
+
{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA,+BAAiC;AACV,sFADd,iBAAU,OACS"}
|
package/errors.js
CHANGED
|
@@ -1,78 +1,27 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
var __extends = (this && this.__extends) || (function () {
|
|
3
|
-
var extendStatics = function (d, b) {
|
|
4
|
-
extendStatics = Object.setPrototypeOf ||
|
|
5
|
-
({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
|
|
6
|
-
function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
|
|
7
|
-
return extendStatics(d, b);
|
|
8
|
-
};
|
|
9
|
-
return function (d, b) {
|
|
10
|
-
if (typeof b !== "function" && b !== null)
|
|
11
|
-
throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
|
|
12
|
-
extendStatics(d, b);
|
|
13
|
-
function __() { this.constructor = d; }
|
|
14
|
-
d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
|
|
15
|
-
};
|
|
16
|
-
})();
|
|
17
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
18
|
-
exports.CramArgumentError = exports.CramSizeLimitError = exports.
|
|
19
|
-
|
|
20
|
-
|
|
21
|
-
function CramError() {
|
|
22
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
23
|
-
}
|
|
24
|
-
return CramError;
|
|
25
|
-
}(Error));
|
|
3
|
+
exports.CramArgumentError = exports.CramSizeLimitError = exports.CramMalformedError = exports.CramUnimplementedError = exports.CramError = void 0;
|
|
4
|
+
class CramError extends Error {
|
|
5
|
+
}
|
|
26
6
|
exports.CramError = CramError;
|
|
27
7
|
/** Error caused by encountering a part of the CRAM spec that has not yet been implemented */
|
|
28
|
-
|
|
29
|
-
|
|
30
|
-
function CramUnimplementedError() {
|
|
31
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
32
|
-
}
|
|
33
|
-
return CramUnimplementedError;
|
|
34
|
-
}(Error));
|
|
8
|
+
class CramUnimplementedError extends Error {
|
|
9
|
+
}
|
|
35
10
|
exports.CramUnimplementedError = CramUnimplementedError;
|
|
36
11
|
/** An error caused by malformed data. */
|
|
37
|
-
|
|
38
|
-
|
|
39
|
-
function CramMalformedError() {
|
|
40
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
41
|
-
}
|
|
42
|
-
return CramMalformedError;
|
|
43
|
-
}(CramError));
|
|
12
|
+
class CramMalformedError extends CramError {
|
|
13
|
+
}
|
|
44
14
|
exports.CramMalformedError = CramMalformedError;
|
|
45
|
-
/**
|
|
46
|
-
* An error caused by attempting to read beyond the end of the defined data.
|
|
47
|
-
*/
|
|
48
|
-
var CramBufferOverrunError = /** @class */ (function (_super) {
|
|
49
|
-
__extends(CramBufferOverrunError, _super);
|
|
50
|
-
function CramBufferOverrunError() {
|
|
51
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
52
|
-
}
|
|
53
|
-
return CramBufferOverrunError;
|
|
54
|
-
}(CramMalformedError));
|
|
55
|
-
exports.CramBufferOverrunError = CramBufferOverrunError;
|
|
56
15
|
/**
|
|
57
16
|
* An error caused by data being too big, exceeding a size limit.
|
|
58
17
|
*/
|
|
59
|
-
|
|
60
|
-
|
|
61
|
-
function CramSizeLimitError() {
|
|
62
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
63
|
-
}
|
|
64
|
-
return CramSizeLimitError;
|
|
65
|
-
}(CramError));
|
|
18
|
+
class CramSizeLimitError extends CramError {
|
|
19
|
+
}
|
|
66
20
|
exports.CramSizeLimitError = CramSizeLimitError;
|
|
67
21
|
/**
|
|
68
22
|
* An invalid argument was supplied to a cram-js method or object.
|
|
69
23
|
*/
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
function CramArgumentError() {
|
|
73
|
-
return _super !== null && _super.apply(this, arguments) || this;
|
|
74
|
-
}
|
|
75
|
-
return CramArgumentError;
|
|
76
|
-
}(CramError));
|
|
24
|
+
class CramArgumentError extends CramError {
|
|
25
|
+
}
|
|
77
26
|
exports.CramArgumentError = CramArgumentError;
|
|
78
27
|
//# sourceMappingURL=errors.js.map
|
package/esm/craiIndex.d.ts
CHANGED
|
@@ -1,4 +1,15 @@
|
|
|
1
|
+
import { CramFileSource } from './cramFile/file';
|
|
2
|
+
export declare type Slice = {
|
|
3
|
+
start: number;
|
|
4
|
+
span: number;
|
|
5
|
+
containerStart: number;
|
|
6
|
+
sliceStart: number;
|
|
7
|
+
sliceBytes: number;
|
|
8
|
+
};
|
|
9
|
+
declare type ParsedIndex = Record<string, Slice[]>;
|
|
1
10
|
export default class CraiIndex {
|
|
11
|
+
private _parseCache;
|
|
12
|
+
private filehandle;
|
|
2
13
|
/**
|
|
3
14
|
*
|
|
4
15
|
* @param {object} args
|
|
@@ -6,21 +17,17 @@ export default class CraiIndex {
|
|
|
6
17
|
* @param {string} [args.url]
|
|
7
18
|
* @param {FileHandle} [args.filehandle]
|
|
8
19
|
*/
|
|
9
|
-
constructor(args:
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
})
|
|
14
|
-
_parseCache: AbortablePromiseCache<any, any>;
|
|
15
|
-
readFile: any;
|
|
16
|
-
parseIndex(): any;
|
|
17
|
-
getIndex(opts?: {}): Promise<any>;
|
|
20
|
+
constructor(args: CramFileSource);
|
|
21
|
+
parseIndex(): Promise<ParsedIndex>;
|
|
22
|
+
getIndex(opts?: {
|
|
23
|
+
signal?: AbortSignal;
|
|
24
|
+
}): Promise<ParsedIndex>;
|
|
18
25
|
/**
|
|
19
26
|
* @param {number} seqId
|
|
20
27
|
* @returns {Promise} true if the index contains entries for
|
|
21
28
|
* the given reference sequence ID, false otherwise
|
|
22
29
|
*/
|
|
23
|
-
hasDataForReferenceSequence(seqId: number): Promise<
|
|
30
|
+
hasDataForReferenceSequence(seqId: number): Promise<boolean>;
|
|
24
31
|
/**
|
|
25
32
|
* fetch index entries for the given range
|
|
26
33
|
*
|
|
@@ -32,6 +39,6 @@ export default class CraiIndex {
|
|
|
32
39
|
* an array of objects of the form
|
|
33
40
|
* `{start, span, containerStart, sliceStart, sliceBytes }`
|
|
34
41
|
*/
|
|
35
|
-
getEntriesForRange(seqId: number, queryStart: number, queryEnd: number): Promise<
|
|
42
|
+
getEntriesForRange(seqId: number, queryStart: number, queryEnd: number): Promise<Slice[]>;
|
|
36
43
|
}
|
|
37
|
-
|
|
44
|
+
export {};
|