@gmod/cram 6.0.0 → 7.0.0
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 +2 -2
- package/dist/craiIndex.js.map +1 -1
- package/dist/cram-bundle.js +1 -1
- package/dist/cramFile/file.d.ts +2 -2
- package/dist/cramFile/file.js +9 -13
- package/dist/cramFile/file.js.map +1 -1
- package/dist/htscodecs/index.d.ts +1 -5
- package/dist/htscodecs/index.js +11 -72
- package/dist/htscodecs/index.js.map +1 -1
- package/dist/htscodecs-wasm.d.ts +7 -0
- package/dist/htscodecs-wasm.js +183 -0
- package/dist/htscodecs-wasm.js.map +1 -0
- package/dist/unzip.d.ts +1 -1
- package/dist/unzip.js +3 -3
- package/dist/unzip.js.map +1 -1
- package/dist/wasm/htscodecs.d.ts +5 -0
- package/dist/wasm/htscodecs.js +0 -0
- package/dist/wasm/htscodecs.js.map +1 -0
- package/esm/craiIndex.js +2 -2
- package/esm/craiIndex.js.map +1 -1
- package/esm/cramFile/file.d.ts +2 -2
- package/esm/cramFile/file.js +7 -11
- package/esm/cramFile/file.js.map +1 -1
- package/esm/htscodecs/index.d.ts +1 -5
- package/esm/htscodecs/index.js +3 -31
- package/esm/htscodecs/index.js.map +1 -1
- package/esm/htscodecs-wasm.d.ts +7 -0
- package/esm/htscodecs-wasm.js +171 -0
- package/esm/htscodecs-wasm.js.map +1 -0
- package/esm/unzip.d.ts +1 -1
- package/esm/unzip.js +3 -3
- package/esm/unzip.js.map +1 -1
- package/esm/wasm/htscodecs.d.ts +5 -0
- package/esm/wasm/htscodecs.js +0 -0
- package/esm/wasm/htscodecs.js.map +1 -0
- package/package.json +9 -9
- package/src/craiIndex.ts +4 -2
- package/src/cramFile/file.ts +7 -11
- package/src/htscodecs/index.ts +12 -38
- package/src/htscodecs-wasm.ts +210 -0
- package/src/unzip.ts +3 -3
- package/src/wasm/htscodecs.d.ts +58 -0
- package/src/wasm/htscodecs.js +0 -0
- package/dist/htscodecs/arith_gen.d.ts +0 -16
- package/dist/htscodecs/arith_gen.js +0 -323
- package/dist/htscodecs/arith_gen.js.map +0 -1
- package/dist/htscodecs/arith_sh.d.ts +0 -9
- package/dist/htscodecs/arith_sh.js +0 -134
- package/dist/htscodecs/arith_sh.js.map +0 -1
- package/dist/htscodecs/byte_model.d.ts +0 -6
- package/dist/htscodecs/byte_model.js +0 -121
- package/dist/htscodecs/byte_model.js.map +0 -1
- package/dist/htscodecs/fqzcomp.d.ts +0 -1
- package/dist/htscodecs/fqzcomp.js +0 -346
- package/dist/htscodecs/fqzcomp.js.map +0 -1
- package/dist/htscodecs/iostream.d.ts +0 -16
- package/dist/htscodecs/iostream.js +0 -148
- package/dist/htscodecs/iostream.js.map +0 -1
- package/dist/htscodecs/rans.d.ts +0 -1
- package/dist/htscodecs/rans.js +0 -224
- package/dist/htscodecs/rans.js.map +0 -1
- package/dist/htscodecs/rans4x16.d.ts +0 -1
- package/dist/htscodecs/rans4x16.js +0 -445
- package/dist/htscodecs/rans4x16.js.map +0 -1
- package/dist/htscodecs/tok3.d.ts +0 -1
- package/dist/htscodecs/tok3.js +0 -206
- package/dist/htscodecs/tok3.js.map +0 -1
- package/dist/rans/constants.d.ts +0 -4
- package/dist/rans/constants.js +0 -10
- package/dist/rans/constants.js.map +0 -1
- package/dist/rans/d04.d.ts +0 -1
- package/dist/rans/d04.js +0 -100
- package/dist/rans/d04.js.map +0 -1
- package/dist/rans/d14.d.ts +0 -1
- package/dist/rans/d14.js +0 -96
- package/dist/rans/d14.js.map +0 -1
- package/dist/rans/decoding.d.ts +0 -27
- package/dist/rans/decoding.js +0 -119
- package/dist/rans/decoding.js.map +0 -1
- package/dist/rans/frequencies.d.ts +0 -2
- package/dist/rans/frequencies.js +0 -112
- package/dist/rans/frequencies.js.map +0 -1
- package/dist/rans/index.d.ts +0 -1
- package/dist/rans/index.js +0 -198
- package/dist/rans/index.js.map +0 -1
- package/dist/seek-bzip/bitreader.d.ts +0 -27
- package/dist/seek-bzip/bitreader.js +0 -101
- package/dist/seek-bzip/bitreader.js.map +0 -1
- package/dist/seek-bzip/crc32.d.ts +0 -26
- package/dist/seek-bzip/crc32.js +0 -115
- package/dist/seek-bzip/crc32.js.map +0 -1
- package/dist/seek-bzip/index.d.ts +0 -9
- package/dist/seek-bzip/index.js +0 -585
- package/dist/seek-bzip/index.js.map +0 -1
- package/dist/seek-bzip/stream.d.ts +0 -8
- package/dist/seek-bzip/stream.js +0 -37
- package/dist/seek-bzip/stream.js.map +0 -1
- package/dist/seek-bzip/toHex.d.ts +0 -1
- package/dist/seek-bzip/toHex.js +0 -36
- package/dist/seek-bzip/toHex.js.map +0 -1
- package/esm/htscodecs/arith_gen.d.ts +0 -16
- package/esm/htscodecs/arith_gen.js +0 -317
- package/esm/htscodecs/arith_gen.js.map +0 -1
- package/esm/htscodecs/arith_sh.d.ts +0 -9
- package/esm/htscodecs/arith_sh.js +0 -131
- package/esm/htscodecs/arith_sh.js.map +0 -1
- package/esm/htscodecs/byte_model.d.ts +0 -6
- package/esm/htscodecs/byte_model.js +0 -118
- package/esm/htscodecs/byte_model.js.map +0 -1
- package/esm/htscodecs/fqzcomp.d.ts +0 -1
- package/esm/htscodecs/fqzcomp.js +0 -340
- package/esm/htscodecs/fqzcomp.js.map +0 -1
- package/esm/htscodecs/iostream.d.ts +0 -16
- package/esm/htscodecs/iostream.js +0 -145
- package/esm/htscodecs/iostream.js.map +0 -1
- package/esm/htscodecs/rans.d.ts +0 -1
- package/esm/htscodecs/rans.js +0 -218
- package/esm/htscodecs/rans.js.map +0 -1
- package/esm/htscodecs/rans4x16.d.ts +0 -1
- package/esm/htscodecs/rans4x16.js +0 -439
- package/esm/htscodecs/rans4x16.js.map +0 -1
- package/esm/htscodecs/tok3.d.ts +0 -1
- package/esm/htscodecs/tok3.js +0 -167
- package/esm/htscodecs/tok3.js.map +0 -1
- package/esm/rans/constants.d.ts +0 -4
- package/esm/rans/constants.js +0 -5
- package/esm/rans/constants.js.map +0 -1
- package/esm/rans/d04.d.ts +0 -1
- package/esm/rans/d04.js +0 -94
- package/esm/rans/d04.js.map +0 -1
- package/esm/rans/d14.d.ts +0 -1
- package/esm/rans/d14.js +0 -93
- package/esm/rans/d14.js.map +0 -1
- package/esm/rans/decoding.d.ts +0 -27
- package/esm/rans/decoding.js +0 -117
- package/esm/rans/decoding.js.map +0 -1
- package/esm/rans/frequencies.d.ts +0 -2
- package/esm/rans/frequencies.js +0 -105
- package/esm/rans/frequencies.js.map +0 -1
- package/esm/rans/index.d.ts +0 -1
- package/esm/rans/index.js +0 -192
- package/esm/rans/index.js.map +0 -1
- package/esm/seek-bzip/bitreader.d.ts +0 -27
- package/esm/seek-bzip/bitreader.js +0 -98
- package/esm/seek-bzip/bitreader.js.map +0 -1
- package/esm/seek-bzip/crc32.d.ts +0 -26
- package/esm/seek-bzip/crc32.js +0 -112
- package/esm/seek-bzip/crc32.js.map +0 -1
- package/esm/seek-bzip/index.d.ts +0 -9
- package/esm/seek-bzip/index.js +0 -579
- package/esm/seek-bzip/index.js.map +0 -1
- package/esm/seek-bzip/stream.d.ts +0 -8
- package/esm/seek-bzip/stream.js +0 -34
- package/esm/seek-bzip/stream.js.map +0 -1
- package/esm/seek-bzip/toHex.d.ts +0 -1
- package/esm/seek-bzip/toHex.js +0 -33
- package/esm/seek-bzip/toHex.js.map +0 -1
- package/src/htscodecs/arith_gen.ts +0 -371
- package/src/htscodecs/arith_sh.ts +0 -146
- package/src/htscodecs/byte_model.ts +0 -136
- package/src/htscodecs/fqzcomp.ts +0 -394
- package/src/htscodecs/iostream.ts +0 -159
- package/src/htscodecs/rans.ts +0 -250
- package/src/htscodecs/rans4x16.ts +0 -521
- package/src/htscodecs/tok3.ts +0 -197
- package/src/rans/README.md +0 -1
- package/src/rans/constants.ts +0 -5
- package/src/rans/d04.ts +0 -112
- package/src/rans/d14.ts +0 -106
- package/src/rans/decoding.ts +0 -138
- package/src/rans/frequencies.ts +0 -115
- package/src/rans/index.ts +0 -245
- package/src/seek-bzip/README.md +0 -6
- package/src/seek-bzip/bitreader.ts +0 -113
- package/src/seek-bzip/crc32.ts +0 -121
- package/src/seek-bzip/index.ts +0 -615
- package/src/seek-bzip/stream.ts +0 -33
- package/src/seek-bzip/toHex.ts +0 -33
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v >>= 4;
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174
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}
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175
|
-
}
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176
|
-
return out;
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177
|
-
}
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|
178
|
-
function RansDecodeStripe(src, len) {
|
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179
|
-
const N = src.ReadByte();
|
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180
|
-
// Retrieve lengths
|
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181
|
-
const clen = new Array(N);
|
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182
|
-
const ulen = new Array(N);
|
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183
|
-
for (var j = 0; j < N; j++) {
|
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184
|
-
clen[j] = src.ReadUint7();
|
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185
|
-
}
|
|
186
|
-
// Decode streams
|
|
187
|
-
const T = new Array(N);
|
|
188
|
-
for (var j = 0; j < N; j++) {
|
|
189
|
-
ulen[j] = Math.floor(len / N) + (len % N > j);
|
|
190
|
-
T[j] = RansDecodeStream(src, ulen[j]);
|
|
191
|
-
}
|
|
192
|
-
// Transpose
|
|
193
|
-
const out = new Uint8Array(len);
|
|
194
|
-
for (var j = 0; j < N; j++) {
|
|
195
|
-
for (let i = 0; i < ulen[j]; i++) {
|
|
196
|
-
out[i * N + j] = T[j][i];
|
|
197
|
-
}
|
|
198
|
-
}
|
|
199
|
-
return out;
|
|
200
|
-
}
|
|
201
|
-
// ----------------------------------------------------------------------
|
|
202
|
-
// Main rANS entry function: decodes a compressed src and
|
|
203
|
-
// returns the uncompressed buffer.
|
|
204
|
-
function decode(src) {
|
|
205
|
-
const stream = new iostream_ts_1.default(src);
|
|
206
|
-
return RansDecodeStream(stream, 0);
|
|
207
|
-
}
|
|
208
|
-
function RansDecodeStream(stream, n_out) {
|
|
209
|
-
const format = stream.ReadByte();
|
|
210
|
-
const order = format & 1;
|
|
211
|
-
const x32 = format & 4;
|
|
212
|
-
const stripe = format & 8;
|
|
213
|
-
const nosz = format & 16;
|
|
214
|
-
const cat = format & 32;
|
|
215
|
-
const rle = format & 64;
|
|
216
|
-
const pack = format & 128;
|
|
217
|
-
const Nway = x32 ? 32 : 4;
|
|
218
|
-
if (!nosz) {
|
|
219
|
-
n_out = stream.ReadUint7();
|
|
220
|
-
}
|
|
221
|
-
// N-way interleaving
|
|
222
|
-
if (stripe) {
|
|
223
|
-
return RansDecodeStripe(stream, n_out);
|
|
224
|
-
}
|
|
225
|
-
// Bit packing
|
|
226
|
-
if (pack) {
|
|
227
|
-
var pack_len = n_out;
|
|
228
|
-
var [P, nsym, n_out] = DecodePackMeta(stream);
|
|
229
|
-
}
|
|
230
|
-
// Run length encoding
|
|
231
|
-
if (rle) {
|
|
232
|
-
var rle_len = n_out;
|
|
233
|
-
var [L, rle_meta, n_out] = DecodeRLEMeta(stream, Nway);
|
|
234
|
-
}
|
|
235
|
-
// Uncompress data (all, packed or run literals)
|
|
236
|
-
if (cat) {
|
|
237
|
-
var buf = stream.ReadData(n_out);
|
|
238
|
-
}
|
|
239
|
-
else if (order == 0) {
|
|
240
|
-
var buf = RansDecode0(stream, n_out, Nway);
|
|
241
|
-
}
|
|
242
|
-
else {
|
|
243
|
-
var buf = RansDecode1(stream, n_out, Nway);
|
|
244
|
-
}
|
|
245
|
-
// Apply expansion transforms
|
|
246
|
-
if (rle) {
|
|
247
|
-
buf = DecodeRLE(buf, L, rle_meta, rle_len);
|
|
248
|
-
}
|
|
249
|
-
if (pack) {
|
|
250
|
-
buf = DecodePack(buf, P, nsym, pack_len);
|
|
251
|
-
}
|
|
252
|
-
return buf;
|
|
253
|
-
}
|
|
254
|
-
// ----------------------------------------------------------------------
|
|
255
|
-
// Order-0 decoder
|
|
256
|
-
function ReadAlphabet(src) {
|
|
257
|
-
const A = new Array(256);
|
|
258
|
-
for (let i = 0; i < 256; i++) {
|
|
259
|
-
A[i] = 0;
|
|
260
|
-
}
|
|
261
|
-
let rle = 0;
|
|
262
|
-
let sym = src.ReadByte();
|
|
263
|
-
let last_sym = sym;
|
|
264
|
-
do {
|
|
265
|
-
A[sym] = 1;
|
|
266
|
-
if (rle > 0) {
|
|
267
|
-
rle--;
|
|
268
|
-
sym++;
|
|
269
|
-
}
|
|
270
|
-
else {
|
|
271
|
-
sym = src.ReadByte();
|
|
272
|
-
if (sym == last_sym + 1) {
|
|
273
|
-
rle = src.ReadByte();
|
|
274
|
-
}
|
|
275
|
-
}
|
|
276
|
-
last_sym = sym;
|
|
277
|
-
} while (sym != 0);
|
|
278
|
-
return A;
|
|
279
|
-
}
|
|
280
|
-
// Decode a single table of order-0 frequencies,
|
|
281
|
-
// filling out the F and C arrays.
|
|
282
|
-
function ReadFrequencies0(src, F, C) {
|
|
283
|
-
// Initialise; not in the specification - implicit?
|
|
284
|
-
for (var i = 0; i < 256; i++) {
|
|
285
|
-
F[i] = 0;
|
|
286
|
-
}
|
|
287
|
-
// Fetch alphabet
|
|
288
|
-
const A = ReadAlphabet(src);
|
|
289
|
-
// Fetch frequencies for the symbols listed in our alphabet
|
|
290
|
-
for (var i = 0; i < 256; i++) {
|
|
291
|
-
if (A[i] > 0) {
|
|
292
|
-
F[i] = src.ReadUint7();
|
|
293
|
-
}
|
|
294
|
-
}
|
|
295
|
-
NormaliseFrequencies0_Shift(F, 12);
|
|
296
|
-
// Compute C[] from F[]
|
|
297
|
-
C[0] = 0;
|
|
298
|
-
for (var i = 0; i <= 255; i++) {
|
|
299
|
-
C[i + 1] = C[i] + F[i];
|
|
300
|
-
}
|
|
301
|
-
}
|
|
302
|
-
function RansDecode0(src, nbytes, N) {
|
|
303
|
-
// Decode frequencies
|
|
304
|
-
const F = new Array(256);
|
|
305
|
-
const C = new Array(256);
|
|
306
|
-
ReadFrequencies0(src, F, C);
|
|
307
|
-
// Fast lookup to avoid slow RansGetSymbolFromFreq
|
|
308
|
-
const C2S = RansBuildC2S(C, 12);
|
|
309
|
-
// Initialise rANS state
|
|
310
|
-
const R = new Array(N);
|
|
311
|
-
for (var i = 0; i < N; i++) {
|
|
312
|
-
R[i] = src.ReadUint32();
|
|
313
|
-
}
|
|
314
|
-
// Main decode loop
|
|
315
|
-
const output = new Uint8Array(nbytes);
|
|
316
|
-
for (var i = 0; i < nbytes; i++) {
|
|
317
|
-
const ix = i & (N - 1); // equiv to i%N as N is power of 2
|
|
318
|
-
const f = RansGetCumulativeFreq(R[ix], 12);
|
|
319
|
-
const s = C2S[f]; // Equiv to RansGetSymbolFromFreq(C, f);
|
|
320
|
-
output[i] = s;
|
|
321
|
-
R[ix] = RansAdvanceStep(R[ix], C[s], F[s], 12);
|
|
322
|
-
R[ix] = RansRenorm(src, R[ix]);
|
|
323
|
-
}
|
|
324
|
-
// Main decode loop
|
|
325
|
-
return output;
|
|
326
|
-
}
|
|
327
|
-
function NormaliseFrequencies0_Shift(F, bits) {
|
|
328
|
-
// Compute total and number of bits to shift by
|
|
329
|
-
let tot = 0;
|
|
330
|
-
for (var i = 0; i < 256; i++) {
|
|
331
|
-
tot += F[i];
|
|
332
|
-
}
|
|
333
|
-
if (tot == 0 || tot == 1 << bits) {
|
|
334
|
-
return;
|
|
335
|
-
}
|
|
336
|
-
let shift = 0;
|
|
337
|
-
while (tot < 1 << bits) {
|
|
338
|
-
tot *= 2;
|
|
339
|
-
shift++;
|
|
340
|
-
}
|
|
341
|
-
// Scale total of frequencies to (1<<bits)
|
|
342
|
-
for (var i = 0; i < 256; i++) {
|
|
343
|
-
F[i] <<= shift;
|
|
344
|
-
}
|
|
345
|
-
}
|
|
346
|
-
// ----------------------------------------------------------------------
|
|
347
|
-
// Order-1 decoder
|
|
348
|
-
// Decode a table of order-1 frequencies,
|
|
349
|
-
// filling out the F and C arrays.
|
|
350
|
-
function ReadFrequencies1(src, F, C, shift) {
|
|
351
|
-
// Initialise; not in the specification - implicit?
|
|
352
|
-
for (var i = 0; i < 256; i++) {
|
|
353
|
-
F[i] = new Array(256);
|
|
354
|
-
C[i] = new Array(256);
|
|
355
|
-
for (var j = 0; j < 256; j++) {
|
|
356
|
-
F[i][j] = 0;
|
|
357
|
-
}
|
|
358
|
-
}
|
|
359
|
-
// Fetch alphabet
|
|
360
|
-
const A = ReadAlphabet(src);
|
|
361
|
-
// Read F[]
|
|
362
|
-
for (var i = 0; i < 256; i++) {
|
|
363
|
-
if (!A[i]) {
|
|
364
|
-
continue;
|
|
365
|
-
}
|
|
366
|
-
let run = 0;
|
|
367
|
-
for (var j = 0; j < 256; j++) {
|
|
368
|
-
if (!A[j]) {
|
|
369
|
-
continue;
|
|
370
|
-
}
|
|
371
|
-
if (run > 0) {
|
|
372
|
-
run--;
|
|
373
|
-
}
|
|
374
|
-
else {
|
|
375
|
-
F[i][j] = src.ReadUint7();
|
|
376
|
-
if (F[i][j] == 0) {
|
|
377
|
-
run = src.ReadByte();
|
|
378
|
-
}
|
|
379
|
-
}
|
|
380
|
-
}
|
|
381
|
-
NormaliseFrequencies0_Shift(F[i], shift);
|
|
382
|
-
// Compute C[] from F[]
|
|
383
|
-
C[i][0] = 0;
|
|
384
|
-
for (var j = 0; j < 256; j++) {
|
|
385
|
-
C[i][j + 1] = C[i][j] + F[i][j];
|
|
386
|
-
}
|
|
387
|
-
}
|
|
388
|
-
}
|
|
389
|
-
function RansDecode1(src, nbytes, N) {
|
|
390
|
-
// FIXME: this bit is missing from the RansDecode0 pseudocode.
|
|
391
|
-
var comp = src.ReadByte();
|
|
392
|
-
const shift = comp >> 4;
|
|
393
|
-
var freq_src = src;
|
|
394
|
-
if (comp & 1) {
|
|
395
|
-
const ulen = src.ReadUint7();
|
|
396
|
-
const clen = src.ReadUint7();
|
|
397
|
-
var comp = new iostream_ts_1.default(src.ReadData(clen));
|
|
398
|
-
var freq_src = new iostream_ts_1.default(RansDecode0(comp, ulen, 4));
|
|
399
|
-
}
|
|
400
|
-
// Decode frequencies
|
|
401
|
-
const F = new Array(256);
|
|
402
|
-
const C = new Array(256);
|
|
403
|
-
ReadFrequencies1(freq_src, F, C, shift);
|
|
404
|
-
// Fast lookup to avoid slow RansGetSymbolFromFreq
|
|
405
|
-
const C2S = new Array(256);
|
|
406
|
-
for (var i = 0; i < 256; i++ // Could do only for symbols in alphabet?
|
|
407
|
-
) {
|
|
408
|
-
C2S[i] = RansBuildC2S(C[i], shift);
|
|
409
|
-
}
|
|
410
|
-
// Initialise rANS state
|
|
411
|
-
const R = new Array(N);
|
|
412
|
-
const L = new Array(N);
|
|
413
|
-
for (var j = 0; j < N; j++) {
|
|
414
|
-
R[j] = src.ReadUint32();
|
|
415
|
-
L[j] = 0;
|
|
416
|
-
}
|
|
417
|
-
// Main decode loop
|
|
418
|
-
const output = new Uint8Array(nbytes);
|
|
419
|
-
const nbytesx = Math.floor(nbytes / N);
|
|
420
|
-
for (var i = 0; i < nbytesx; i++) {
|
|
421
|
-
for (var j = 0; j < N; j++) {
|
|
422
|
-
var f = RansGetCumulativeFreq(R[j], shift);
|
|
423
|
-
// var s = RansGetSymbolFromFreq(C[L[j]], f);
|
|
424
|
-
var s = C2S[L[j]][f]; // Precomputed version of above
|
|
425
|
-
output[i + j * nbytesx] = s;
|
|
426
|
-
R[j] = RansAdvanceStep(R[j], C[L[j]][s], F[L[j]][s], shift);
|
|
427
|
-
R[j] = RansRenorm(src, R[j]);
|
|
428
|
-
L[j] = s;
|
|
429
|
-
}
|
|
430
|
-
}
|
|
431
|
-
// Now deal with the remainder if buffer size is not a multiple of N,
|
|
432
|
-
// using the last rANS state exclusively. (It'd have been nice to have
|
|
433
|
-
// designed this to just act as if we kept going with a bail out.)
|
|
434
|
-
i = N * i;
|
|
435
|
-
while (i < nbytes) {
|
|
436
|
-
var f = RansGetCumulativeFreq(R[N - 1], shift);
|
|
437
|
-
var s = RansGetSymbolFromFreq(C[L[N - 1]], f);
|
|
438
|
-
output[i++] = s;
|
|
439
|
-
R[N - 1] = RansAdvanceStep(R[N - 1], C[L[N - 1]][s], F[L[N - 1]][s], shift);
|
|
440
|
-
R[N - 1] = RansRenorm(src, R[N - 1]);
|
|
441
|
-
L[N - 1] = s;
|
|
442
|
-
}
|
|
443
|
-
return output;
|
|
444
|
-
}
|
|
445
|
-
//# sourceMappingURL=rans4x16.js.map
|
|
@@ -1 +0,0 @@
|
|
|
1
|
-
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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*
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* 2. Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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*
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* 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
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* Institute nor the names of its contributors may be used to endorse
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* or promote products derived from this software without specific
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* prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
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* IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
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* TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
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* PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
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* LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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74
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// Name tokeniser
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75
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//
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76
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// This is a reference implementation designed to match the
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77
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// written specification as closely as possible. It is *NOT*
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78
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// an efficient implementation, but see comments below.
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79
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const util_ts_1 = require("../util.js");
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const arith_gen_ts_1 = __importDefault(require("./arith_gen.js"));
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81
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-
const iostream_ts_1 = __importDefault(require("./iostream.js"));
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82
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const rans = __importStar(require("./rans4x16.js"));
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83
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const arith = new arith_gen_ts_1.default();
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84
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-
const TOK_TYPE = 0;
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85
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-
const TOK_STRING = 1;
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86
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-
const TOK_CHAR = 2;
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87
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const TOK_DIGITS0 = 3;
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88
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const TOK_DZLEN = 4;
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89
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const TOK_DUP = 5;
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90
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const TOK_DIFF = 6;
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91
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const TOK_DIGITS = 7;
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92
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const TOK_DELTA = 8;
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93
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const TOK_DELTA0 = 9;
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94
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-
const TOK_MATCH = 10;
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95
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-
const TOK_NOP = 11;
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96
|
-
const TOK_END = 12;
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97
|
-
// ----------------------------------------------------------------------
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98
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// Token byte streams
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|
99
|
-
function DecodeTokenByteStreams(src, in_size, use_arith, nnames) {
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|
100
|
-
let t = -1;
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|
101
|
-
const B = new Array(256);
|
|
102
|
-
while (!src.EOF()) {
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103
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-
const ttype = src.ReadByte();
|
|
104
|
-
const tok_new = ttype & 128;
|
|
105
|
-
const tok_dup = ttype & 64;
|
|
106
|
-
const type = ttype & 63;
|
|
107
|
-
if (tok_new) {
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|
108
|
-
t++;
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|
109
|
-
B[t] = new Array(13);
|
|
110
|
-
}
|
|
111
|
-
if (type != TOK_TYPE && tok_new) {
|
|
112
|
-
const M = new Array(nnames - 1).fill(TOK_MATCH);
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|
113
|
-
B[t][TOK_TYPE] = new iostream_ts_1.default((0, util_ts_1.concatUint8Array)([new Uint8Array(type), M]));
|
|
114
|
-
}
|
|
115
|
-
if (tok_dup) {
|
|
116
|
-
const dup_pos = src.ReadByte();
|
|
117
|
-
const dup_type = src.ReadByte();
|
|
118
|
-
B[t][type] = new iostream_ts_1.default(B[dup_pos][dup_type].buf);
|
|
119
|
-
}
|
|
120
|
-
else {
|
|
121
|
-
const clen = src.ReadUint7();
|
|
122
|
-
const data = src.ReadData(clen);
|
|
123
|
-
B[t][type] = use_arith ? arith.decode(data) : rans.decode(data);
|
|
124
|
-
B[t][type] = new iostream_ts_1.default(B[t][type]);
|
|
125
|
-
}
|
|
126
|
-
}
|
|
127
|
-
return B;
|
|
128
|
-
}
|
|
129
|
-
// ----------------------------------------------------------------------
|
|
130
|
-
// Token decode
|
|
131
|
-
function LeftPadNumber(val, len) {
|
|
132
|
-
let str = val + '';
|
|
133
|
-
while (str.length < len) {
|
|
134
|
-
str = '0' + str;
|
|
135
|
-
}
|
|
136
|
-
return str;
|
|
137
|
-
}
|
|
138
|
-
function DecodeSingleName(B, N, T, n) {
|
|
139
|
-
let type = B[0][TOK_TYPE].ReadByte();
|
|
140
|
-
const dist = B[0][type].ReadUint32();
|
|
141
|
-
const m = n - dist;
|
|
142
|
-
if (type == TOK_DUP) {
|
|
143
|
-
N[n] = N[m];
|
|
144
|
-
T[n] = T[m];
|
|
145
|
-
return N[n];
|
|
146
|
-
}
|
|
147
|
-
let t = 1;
|
|
148
|
-
N[n] = '';
|
|
149
|
-
T[n] = new Array(256);
|
|
150
|
-
do {
|
|
151
|
-
type = B[t][TOK_TYPE].ReadByte();
|
|
152
|
-
switch (type) {
|
|
153
|
-
case TOK_CHAR:
|
|
154
|
-
T[n][t] = B[t][TOK_CHAR].ReadChar();
|
|
155
|
-
break;
|
|
156
|
-
case TOK_STRING:
|
|
157
|
-
T[n][t] = B[t][TOK_STRING].ReadString();
|
|
158
|
-
break;
|
|
159
|
-
case TOK_DIGITS:
|
|
160
|
-
T[n][t] = B[t][TOK_DIGITS].ReadUint32();
|
|
161
|
-
break;
|
|
162
|
-
case TOK_DIGITS0:
|
|
163
|
-
var d = B[t][TOK_DIGITS0].ReadUint32();
|
|
164
|
-
var l = B[t][TOK_DZLEN].ReadByte();
|
|
165
|
-
T[n][t] = LeftPadNumber(d, l);
|
|
166
|
-
break;
|
|
167
|
-
case TOK_DELTA:
|
|
168
|
-
T[n][t] = (T[m][t] >> 0) + B[t][TOK_DELTA].ReadByte();
|
|
169
|
-
break;
|
|
170
|
-
case TOK_DELTA0:
|
|
171
|
-
var d = (T[m][t] >> 0) + B[t][TOK_DELTA0].ReadByte();
|
|
172
|
-
var l = T[m][t].length;
|
|
173
|
-
T[n][t] = LeftPadNumber(d, l);
|
|
174
|
-
break;
|
|
175
|
-
case TOK_MATCH:
|
|
176
|
-
T[n][t] = T[m][t];
|
|
177
|
-
break;
|
|
178
|
-
default:
|
|
179
|
-
T[n][t] = '';
|
|
180
|
-
break;
|
|
181
|
-
}
|
|
182
|
-
N[n] += T[n][t++];
|
|
183
|
-
} while (type != TOK_END);
|
|
184
|
-
return N[n];
|
|
185
|
-
}
|
|
186
|
-
// ----------------------------------------------------------------------
|
|
187
|
-
// Main tokeniser decode entry function: decodes a compressed src and
|
|
188
|
-
// returns the uncompressed buffer.
|
|
189
|
-
function decode(src, len, separator) {
|
|
190
|
-
var src = new iostream_ts_1.default(src);
|
|
191
|
-
const ulen = src.ReadUint32();
|
|
192
|
-
const nnames = src.ReadUint32();
|
|
193
|
-
const use_arith = src.ReadByte();
|
|
194
|
-
const B = DecodeTokenByteStreams(src, len, use_arith, nnames);
|
|
195
|
-
const N = new Array(nnames);
|
|
196
|
-
const T = new Array(nnames);
|
|
197
|
-
let str = '';
|
|
198
|
-
if (separator === undefined) {
|
|
199
|
-
separator = '\n';
|
|
200
|
-
}
|
|
201
|
-
for (let i = 0; i < nnames; i++) {
|
|
202
|
-
str += DecodeSingleName(B, N, T, i) + separator;
|
|
203
|
-
}
|
|
204
|
-
return str;
|
|
205
|
-
}
|
|
206
|
-
//# sourceMappingURL=tok3.js.map
|