File: rld0.c

package info (click to toggle)
fermi-lite 0.1-5
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, buster, sid
  • size: 652 kB
  • sloc: ansic: 5,157; makefile: 63; sh: 13
file content (489 lines) | stat: -rw-r--r-- 13,226 bytes parent folder | download | duplicates (4)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
#include <stdlib.h>
#include <stdint.h>
#include <stdio.h>
#include <string.h>
#include <assert.h>
#include <unistd.h>
#include <fcntl.h>
#include <sys/mman.h>
#include "rld0.h"

#define RLD_IBITS_PLUS 4

#define rld_file_size(e) ((4 + (e)->asize) * 8 + (e)->n_bytes + 8 * (e)->n_frames * ((e)->asize + 1))

#ifndef xcalloc
#define xcalloc(n, s) calloc(n, s)
#endif
#ifndef xmalloc
#define xmalloc(s) malloc(s)
#endif

/******************
 * Delta encoding *
 ******************/

static const char LogTable256[256] = {
#define LT(n) n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n
    -1, 0, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3,
    LT(4), LT(5), LT(5), LT(6), LT(6), LT(6), LT(6),
    LT(7), LT(7), LT(7), LT(7), LT(7), LT(7), LT(7), LT(7)
};

static inline int ilog2_32(uint32_t v)
{
	register uint32_t t, tt;
	if ((tt = v>>16)) return (t = tt>>8) ? 24 + LogTable256[t] : 16 + LogTable256[tt];
	return (t = v>>8) ? 8 + LogTable256[t] : LogTable256[v];
}

static inline int ilog2(uint64_t v)
{
	return v>>32? 32 + ilog2_32(v>>32) : ilog2_32(v);
}

static inline int64_t rld_delta_enc1(uint64_t x, int *width)
{
	int y = ilog2(x);
	int z = ilog2_32(y + 1);
	*width = (z<<1) + 1 + y;
	return (x ^ (uint64_t)1<<y) | (uint64_t)(y+1)<<y;
}

/***********************************
 * Initialization and deallocation *
 ***********************************/

rld_t *rld_init(int asize, int bbits)
{
	rld_t *e;
	e = xcalloc(1, sizeof(rld_t));
	e->n = 1;
	e->z = xmalloc(sizeof(void*));
	e->z[0] = xcalloc(RLD_LSIZE, 8);
	e->ssize = 1<<bbits;
	e->cnt = xcalloc(asize + 1, 8);
	e->mcnt = xcalloc(asize + 1, 8);
	e->abits = ilog2(asize) + 1;
	e->asize = asize;
	e->sbits = bbits;
	e->asize1 = asize + 1;
	e->offset0[0] = (e->asize1*16+63)/64;
	e->offset0[1] = (e->asize1*32+63)/64;
	e->offset0[2] = e->asize1;
	return e;
}

void rld_destroy(rld_t *e)
{
	int i = 0;
	if (e == 0) return;
	if (e->mem) {
		close(e->fd);
		munmap(e->mem, rld_file_size(e));
	} else {
		for (i = 0; i < e->n; ++i) free(e->z[i]);
		free(e->frame);
	}
	free(e->z); free(e->cnt); free(e->mcnt); free(e);
}

void rld_itr_init(const rld_t *e, rlditr_t *itr, uint64_t k)
{
	itr->i = e->z + (k >> RLD_LBITS);
	itr->shead = *itr->i + k%RLD_LSIZE;
	itr->stail = rld_get_stail(e, itr);
	itr->p = itr->shead + e->offset0[rld_block_type(*itr->shead)];
	itr->q = (uint8_t*)itr->p;
	itr->r = 64;
	itr->c = -1;
	itr->l = 0;
}

/************
 * Encoding *
 ************/

static inline void enc_next_block(rld_t *e, rlditr_t *itr)
{
	int i, type;
	if (itr->stail + 2 - *itr->i == RLD_LSIZE) {
		++e->n;
		e->z = realloc(e->z, e->n * sizeof(void*));
		itr->i = e->z + e->n - 1;
		itr->shead = *itr->i = xcalloc(RLD_LSIZE, 8);
	} else itr->shead += e->ssize;
	if (e->cnt[0] - e->mcnt[0] < 0x4000) {
		uint16_t *p = (uint16_t*)itr->shead;
		for (i = 0; i <= e->asize; ++i) p[i] = e->cnt[i] - e->mcnt[i];
		type = 0;
	} else if (e->cnt[0] - e->mcnt[0] < 0x40000000) {
		uint32_t *p = (uint32_t*)itr->shead;
		for (i = 0; i <= e->asize; ++i) p[i] = e->cnt[i] - e->mcnt[i];
		type = 1;
	} else {
		uint64_t *p = (uint64_t*)itr->shead;
		for (i = 0; i <= e->asize; ++i) p[i] = e->cnt[i] - e->mcnt[i];
		type = 2;
	}
	*itr->shead |= (uint64_t)type<<62;
	itr->p = itr->shead + e->offset0[type];
	itr->stail = rld_get_stail(e, itr);
	itr->q = (uint8_t*)itr->p;
	itr->r = 64;
	for (i = 0; i <= e->asize; ++i) e->mcnt[i] = e->cnt[i];
}

static int rld_enc1(rld_t *e, rlditr_t *itr, int64_t l, uint8_t c)
{
	int w;
	uint64_t x = rld_delta_enc1(l, &w) << e->abits | c;
	w += e->abits;
	if (w >= itr->r && itr->p == itr->stail) enc_next_block(e, itr);
	if (w > itr->r) {
		w -= itr->r;
		*itr->p++ |= x >> w;
		*itr->p = x << (itr->r = 64 - w);
	} else itr->r -= w, *itr->p |= x << itr->r;
	e->cnt[0] += l;
	e->cnt[c + 1] += l;
	return 0;
}

int rld_enc(rld_t *e, rlditr_t *itr, int64_t l, uint8_t c)
{
	if (l == 0) return 0;
	if (itr->c != c) {
		if (itr->l) rld_enc1(e, itr, itr->l, itr->c);
		itr->l = l; itr->c = c;
	} else itr->l += l;
	return 0;
}

void rld_rank_index(rld_t *e)
{
	uint64_t last, n_blks, i, k, *cnt;
	int j;

	n_blks = e->n_bytes * 8 / 64 / e->ssize + 1;
	last = rld_last_blk(e);
	cnt = alloca(e->asize * 8);
	e->ibits = ilog2(e->mcnt[0] / n_blks) + RLD_IBITS_PLUS;
	e->n_frames = ((e->mcnt[0] + (1ll<<e->ibits) - 1) >> e->ibits) + 1;
	e->frame = xcalloc(e->n_frames * e->asize1, 8);
	e->frame[0] = 0;
	for (j = 0; j < e->asize; ++j) cnt[j] = 0;
	for (i = e->ssize, k = 1; i <= last; i += e->ssize) {
		uint64_t sum, *p = rld_seek_blk(e, i);
		int type = rld_block_type(*p);
		if (type == 0) {
			uint16_t *q = (uint16_t*)p;
			for (j = 1; j <= e->asize; ++j) cnt[j-1] += q[j];
		} else if (type == 1) {
			uint32_t *q = (uint32_t*)p;
			for (j = 1; j <= e->asize; ++j) cnt[j-1] += q[j] & 0x3fffffff;
		} else {
			uint64_t *q = (uint64_t*)p;
			for (j = 1; j <= e->asize; ++j) cnt[j-1] += q[j];
		}
		for (j = 0, sum = 0; j < e->asize; ++j) sum += cnt[j];
		while (sum >= k<<e->ibits) ++k;
		if (k < e->n_frames) {
			uint64_t x = k * e->asize1;
			e->frame[x] = i;
			for (j = 0; j < e->asize; ++j) e->frame[x + j + 1] = cnt[j];
		}
	}
	assert(k >= e->n_frames - 1);
	for (k = 1; k < e->n_frames; ++k) { // fill zero cells
		uint64_t x = k * e->asize1;
		if (e->frame[x] == 0) {
			for (j = 0; j <= e->asize; ++j)
				e->frame[x + j] = e->frame[x - e->asize1 + j];
		}
	}
}

uint64_t rld_enc_finish(rld_t *e, rlditr_t *itr)
{
	int i;
	if (itr->l) rld_enc1(e, itr, itr->l, itr->c);
	enc_next_block(e, itr);
	e->n_bytes = (((uint64_t)(e->n - 1) * RLD_LSIZE) + (itr->p - *itr->i)) * 8;
	// recompute e->cnt as the accumulative count; e->mcnt[] keeps the marginal counts
	for (e->cnt[0] = 0, i = 1; i <= e->asize; ++i) e->cnt[i] += e->cnt[i - 1];
	rld_rank_index(e);
	return e->n_bytes;
}

/*****************
 * Save and load *
 *****************/

int rld_dump(const rld_t *e, const char *fn)
{
	uint64_t k = 0;
	int i;
	uint32_t a;
	FILE *fp;
	fp = strcmp(fn, "-")? fopen(fn, "wb") : fdopen(fileno(stdout), "wb");
	if (fp == 0) return -1;
	a = e->asize<<16 | e->sbits;
	fwrite("RLD\3", 1, 4, fp); // write magic
	fwrite(&a, 4, 1, fp); // write sbits and asize
	fwrite(&k, 8, 1, fp); // preserve 8 bytes for future uses
	fwrite(&e->n_bytes, 8, 1, fp); // n_bytes can always be divided by 8
	fwrite(&e->n_frames, 8, 1, fp); // number of frames
	fwrite(e->mcnt + 1, 8, e->asize, fp); // write the marginal counts
	for (i = 0, k = e->n_bytes / 8; i < e->n - 1; ++i, k -= RLD_LSIZE)
		fwrite(e->z[i], 8, RLD_LSIZE, fp);
	fwrite(e->z[i], 8, k, fp);
	fwrite(e->frame, 8 * e->asize1, e->n_frames, fp);
	fclose(fp);
	return 0;
}

static rld_t *rld_restore_header(const char *fn, FILE **_fp)
{
	FILE *fp;
	rld_t *e;
	char magic[4];
	uint64_t a[3];
	int32_t i, x;

	if (strcmp(fn, "-") == 0) *_fp = fp = stdin;
	else if ((*_fp = fp = fopen(fn, "rb")) == 0) return 0;
	fread(magic, 1, 4, fp);
	if (strncmp(magic, "RLD\3", 4)) return 0;
	fread(&x, 4, 1, fp);
	e = rld_init(x>>16, x&0xffff);
	fread(a, 8, 3, fp);
	e->n_bytes = a[1]; e->n_frames = a[2];
	fread(e->mcnt + 1, 8, e->asize, fp);
	for (i = 0; i <= e->asize; ++i) e->cnt[i] = e->mcnt[i];
	for (i = 1; i <= e->asize; ++i) e->cnt[i] += e->cnt[i - 1];
	e->mcnt[0] = e->cnt[e->asize];
	return e;
}

rld_t *rld_restore(const char *fn)
{
	FILE *fp;
	rld_t *e;
	uint64_t k, n_blks;
	int32_t i;

	if ((e = rld_restore_header(fn, &fp)) == 0) { // then load as plain DNA rle
		uint8_t *buf;
		int l;
		rlditr_t itr;
		buf = malloc(0x10000);
		e = rld_init(6, 3);
		rld_itr_init(e, &itr, 0);
		while ((l = fread(buf, 1, 0x10000, fp)) != 0)
			for (i = 0; i < l; ++i)
				if (buf[i]>>3) rld_enc(e, &itr, buf[i]>>3, buf[i]&7);
		fclose(fp);
		free(buf);
		rld_enc_finish(e, &itr);
		return e;
	}
	if (e->n_bytes / 8 > RLD_LSIZE) { // allocate enough memory
		e->n = (e->n_bytes / 8 + RLD_LSIZE - 1) / RLD_LSIZE;
		e->z = realloc(e->z, e->n * sizeof(void*));
		for (i = 1; i < e->n; ++i)
			e->z[i] = xcalloc(RLD_LSIZE, 8);
	}
	for (i = 0, k = e->n_bytes / 8; i < e->n - 1; ++i, k -= RLD_LSIZE)
		fread(e->z[i], 8, RLD_LSIZE, fp);
	fread(e->z[i], 8, k, fp);
	e->frame = xmalloc(e->n_frames * e->asize1 * 8);
	fread(e->frame, 8 * e->asize1, e->n_frames, fp);
	fclose(fp);
	n_blks = e->n_bytes * 8 / 64 / e->ssize + 1;
	e->ibits = ilog2(e->mcnt[0] / n_blks) + RLD_IBITS_PLUS;
	return e;
}

rld_t *rld_restore_mmap(const char *fn)
{
	FILE *fp;
	rld_t *e;
	int i;
	int64_t n_blks;

	e = rld_restore_header(fn, &fp);
	fclose(fp);
	free(e->z[0]); free(e->z);
	e->n = (e->n_bytes / 8 + RLD_LSIZE - 1) / RLD_LSIZE;
	e->z = xcalloc(e->n, sizeof(void*));
	e->fd = open(fn, O_RDONLY);
	e->mem = (uint64_t*)mmap(0, rld_file_size(e), PROT_READ, MAP_PRIVATE, e->fd, 0);
	for (i = 0; i < e->n; ++i) e->z[i] = e->mem + (4 + e->asize) + (size_t)i * RLD_LSIZE;
	e->frame = e->mem + (4 + e->asize) + e->n_bytes/8;
	n_blks = e->n_bytes * 8 / 64 / e->ssize + 1;
	e->ibits = ilog2(e->mcnt[0] / n_blks) + RLD_IBITS_PLUS;
	return e;
}

/******************
 * Computing rank *
 ******************/

#ifdef _DNA_ONLY
static inline int64_t rld_dec0_fast_dna(const rld_t *e, rlditr_t *itr, int *c)
{ // This is NOT a replacement of rld_dec0(). It does not do boundary check.
	uint64_t x = itr->r == 64? itr->p[0] : itr->p[0] << (64 - itr->r) | itr->p[1] >> itr->r;
	if (x>>63 == 0) {
		int64_t y;
		int l, w = 0x333333335555779bll>>(x>>59<<2)&0xf;
		l = (x >> (64 - w)) - 1;
		y = x << w >> (64 - l) | 1u << l;
		w += l;
		*c = x << w >> 61;
		w += 3;
		itr->r -= w;
		if (itr->r <= 0) ++itr->p, itr->r += 64;
		return y;
	} else {
		*c = x << 1 >> 61;
		itr->r -= 4;
		if (itr->r <= 0) ++itr->p, itr->r += 64;
		return 1;
	}
}
#endif

static inline uint64_t rld_locate_blk(const rld_t *e, rlditr_t *itr, uint64_t k, uint64_t *cnt, uint64_t *sum)
{
	int j;
	uint64_t c = 0, *q, *z = e->frame + (k>>e->ibits) * e->asize1;
	itr->i = e->z + (*z>>RLD_LBITS);
	q = itr->p = *itr->i + (*z&RLD_LMASK);
	for (j = 1, *sum = 0; j < e->asize1; ++j) *sum += (cnt[j-1] = z[j]);
	while (1) { // seek to the small block
		int type;
		q += e->ssize;
		if (q - *itr->i == RLD_LSIZE) q = *++itr->i;
		type = rld_block_type(*q);
		c = type == 2? *q&0x3fffffffffffffffULL : type == 1? *(uint32_t*)q : *(uint16_t*)q;
		if (*sum + c > k) break;
		if (type == 0) {
			uint16_t *p = (uint16_t*)q + 1;
#ifdef _DNA_ONLY
			cnt[0] += p[0]; cnt[1] += p[1]; cnt[2] += p[2]; cnt[3] += p[3]; cnt[4] += p[4]; cnt[5] += p[5];
#else
			for (j = 0; j < e->asize; ++j) cnt[j] += p[j];
#endif
		} else if (type == 1) {
			uint32_t *p = (uint32_t*)q + 1;
			for (j = 0; j < e->asize; ++j) cnt[j] += p[j] & 0x3fffffff;
		} else {
			uint64_t *p = (uint64_t*)q + 1;
			for (j = 0; j < e->asize; ++j) cnt[j] += p[j];
		}
		*sum += c;
		itr->p = q;
	}
	itr->shead = itr->p;
	itr->stail = rld_get_stail(e, itr);
	itr->p += e->offset0[rld_block_type(*itr->shead)];
	itr->q = (uint8_t*)itr->p;
	itr->r = 64;
	return c + *sum;
}

void rld_rank21(const rld_t *e, uint64_t k, uint64_t l, int c, uint64_t *ok, uint64_t *ol) // FIXME: can be faster
{
	*ok = rld_rank11(e, k, c);
	*ol = rld_rank11(e, l, c);
}

int rld_rank1a(const rld_t *e, uint64_t k, uint64_t *ok)
{
	uint64_t z, l;
	int a = -1;
	rlditr_t itr;
	if (k == 0) {
		for (a = 0; a < e->asize; ++a) ok[a] = 0;
		return -1;
	}
	rld_locate_blk(e, &itr, k-1, ok, &z);
	while (1) {
#ifdef _DNA_ONLY
		l = rld_dec0_fast_dna(e, &itr, &a);
#else
		l = rld_dec0(e, &itr, &a);
#endif
		if (z + l >= k) break;
		z += l; ok[a] += l;
	}
	ok[a] += k - z;
	return a;
}

uint64_t rld_rank11(const rld_t *e, uint64_t k, int c)
{
	uint64_t *ok;
	if (k == (uint64_t)-1) return 0;
	ok = alloca(e->asize1 * 8);
	rld_rank1a(e, k, ok);
	return ok[c];
}

void rld_rank2a(const rld_t *e, uint64_t k, uint64_t l, uint64_t *ok, uint64_t *ol)
{
	uint64_t z, y, len;
	rlditr_t itr;
	int a = -1;
	if (k == 0) {
		for (a = 0; a < e->asize; ++a) ok[a] = 0;
		rld_rank1a(e, l, ol);
		return;
	}
	y = rld_locate_blk(e, &itr, k-1, ok, &z); // locate the block bracketing k
	while (1) { // compute ok[]
#ifdef _DNA_ONLY
		len = rld_dec0_fast_dna(e, &itr, &a);
#else
		len = rld_dec0(e, &itr, &a);
#endif
		if (z + len >= k) break;
		z += len; ok[a] += len;
	}
	if (y > l) { // we do not need to decode other blocks
		int b;
		for (b = 0; b < e->asize; ++b) ol[b] = ok[b]; // copy ok[] to ol[]
		ok[a] += k - z; // finalize ok[a]
		if (z + len < l) { // we need to decode the next run
			z += len; ol[a] += len;
			while (1) {
				len = rld_dec0(e, &itr, &a);
				if (z + len >= l) break;
				z += len; ol[a] += len;
			}
		}
		ol[a] += l - z;
	} else { // we have to decode other blocks
		ok[a] += k - z;
		rld_rank1a(e, l, ol);
	}
}

int rld_extend(const rld_t *e, const rldintv_t *ik, rldintv_t ok[6], int is_back)
{ // TODO: this can be accelerated a little by using rld_rank1a() when ik.x[2]==1
	uint64_t tk[6], tl[6];
	int i;
	rld_rank2a(e, ik->x[!is_back], ik->x[!is_back] + ik->x[2], tk, tl);
	for (i = 0; i < 6; ++i) {
		ok[i].x[!is_back] = e->cnt[i] + tk[i];
		ok[i].x[2] = (tl[i] -= tk[i]);
	}
	ok[0].x[is_back] = ik->x[is_back];
	ok[4].x[is_back] = ok[0].x[is_back] + tl[0];
	ok[3].x[is_back] = ok[4].x[is_back] + tl[4];
	ok[2].x[is_back] = ok[3].x[is_back] + tl[3];
	ok[1].x[is_back] = ok[2].x[is_back] + tl[2];
	ok[5].x[is_back] = ok[1].x[is_back] + tl[1];
	return 0;
}