HsHTSLib-1.3.2.0: htslib-1.3.2/cram/rANS_static.c
/*
* Copyright (c) 2014 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
*
* 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
* Institute nor the names of its contributors may be used to endorse
* or promote products derived from this software without specific
* prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
* IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
* TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
* PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
* LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
/*
* Author: James Bonfield, Wellcome Trust Sanger Institute. 2014
*/
#include <config.h>
#include <stdint.h>
#include <stdlib.h>
#include <stdio.h>
#include <unistd.h>
#include <assert.h>
#include <string.h>
#include <sys/time.h>
#include "cram/rANS_static.h"
#include "cram/rANS_byte.h"
#define TF_SHIFT 12
#define TOTFREQ (1<<TF_SHIFT)
#define ABS(a) ((a)>0?(a):-(a))
#ifndef BLK_SIZE
# define BLK_SIZE 1024*1024
#endif
// Room to allow for expanded BLK_SIZE on worst case compression.
#define BLK_SIZE2 ((int)(1.05*BLK_SIZE))
/*-----------------------------------------------------------------------------
* Memory to memory compression functions.
*
* These are original versions without any manual loop unrolling. They
* are easier to understand, but can be up to 2x slower.
*/
unsigned char *rans_compress_O0(unsigned char *in, unsigned int in_size,
unsigned int *out_size) {
unsigned char *out_buf = malloc(1.05*in_size + 257*257*3 + 9);
unsigned char *cp, *out_end;
RansEncSymbol syms[256];
RansState rans0, rans1, rans2, rans3;
uint8_t* ptr;
int F[256] = {0}, i, j, tab_size, rle, x, fsum = 0;
int m = 0, M = 0;
uint64_t tr;
if (!out_buf)
return NULL;
ptr = out_end = out_buf + (int)(1.05*in_size) + 257*257*3 + 9;
// Compute statistics
for (i = 0; i < in_size; i++) {
F[in[i]]++;
}
tr = ((uint64_t)TOTFREQ<<31)/in_size + (1<<30)/in_size;
// Normalise so T[i] == TOTFREQ
for (m = M = j = 0; j < 256; j++) {
if (!F[j])
continue;
if (m < F[j])
m = F[j], M = j;
if ((F[j] = (F[j]*tr)>>31) == 0)
F[j] = 1;
fsum += F[j];
}
fsum++;
if (fsum < TOTFREQ)
F[M] += TOTFREQ-fsum;
else
F[M] -= fsum-TOTFREQ;
//printf("F[%d]=%d\n", M, F[M]);
assert(F[M]>0);
// Encode statistics.
cp = out_buf+9;
for (x = rle = j = 0; j < 256; j++) {
if (F[j]) {
// j
if (rle) {
rle--;
} else {
*cp++ = j;
if (!rle && j && F[j-1]) {
for(rle=j+1; rle<256 && F[rle]; rle++)
;
rle -= j+1;
*cp++ = rle;
}
//fprintf(stderr, "%d: %d %d\n", j, rle, N[j]);
}
// F[j]
if (F[j]<128) {
*cp++ = F[j];
} else {
*cp++ = 128 | (F[j]>>8);
*cp++ = F[j]&0xff;
}
RansEncSymbolInit(&syms[j], x, F[j], TF_SHIFT);
x += F[j];
}
}
*cp++ = 0;
//write(1, out_buf+4, cp-(out_buf+4));
tab_size = cp-out_buf;
RansEncInit(&rans0);
RansEncInit(&rans1);
RansEncInit(&rans2);
RansEncInit(&rans3);
switch (i=(in_size&3)) {
case 3: RansEncPutSymbol(&rans2, &ptr, &syms[in[in_size-(i-2)]]);
case 2: RansEncPutSymbol(&rans1, &ptr, &syms[in[in_size-(i-1)]]);
case 1: RansEncPutSymbol(&rans0, &ptr, &syms[in[in_size-(i-0)]]);
case 0:
break;
}
for (i=(in_size &~3); i>0; i-=4) {
RansEncSymbol *s3 = &syms[in[i-1]];
RansEncSymbol *s2 = &syms[in[i-2]];
RansEncSymbol *s1 = &syms[in[i-3]];
RansEncSymbol *s0 = &syms[in[i-4]];
RansEncPutSymbol(&rans3, &ptr, s3);
RansEncPutSymbol(&rans2, &ptr, s2);
RansEncPutSymbol(&rans1, &ptr, s1);
RansEncPutSymbol(&rans0, &ptr, s0);
}
RansEncFlush(&rans3, &ptr);
RansEncFlush(&rans2, &ptr);
RansEncFlush(&rans1, &ptr);
RansEncFlush(&rans0, &ptr);
// Finalise block size and return it
*out_size = (out_end - ptr) + tab_size;
cp = out_buf;
*cp++ = 0; // order
*cp++ = ((*out_size-9)>> 0) & 0xff;
*cp++ = ((*out_size-9)>> 8) & 0xff;
*cp++ = ((*out_size-9)>>16) & 0xff;
*cp++ = ((*out_size-9)>>24) & 0xff;
*cp++ = (in_size>> 0) & 0xff;
*cp++ = (in_size>> 8) & 0xff;
*cp++ = (in_size>>16) & 0xff;
*cp++ = (in_size>>24) & 0xff;
memmove(out_buf + tab_size, ptr, out_end-ptr);
return out_buf;
}
typedef struct {
struct {
int F;
int C;
} fc[256];
unsigned char *R;
} ari_decoder;
unsigned char *rans_uncompress_O0(unsigned char *in, unsigned int in_size,
unsigned int *out_size) {
/* Load in the static tables */
unsigned char *cp = in + 9;
int i, j, x, out_sz, in_sz, rle;
char *out_buf;
ari_decoder D;
RansDecSymbol syms[256];
memset(&D, 0, sizeof(D));
if (*in++ != 0) // Order-0 check
return NULL;
in_sz = ((in[0])<<0) | ((in[1])<<8) | ((in[2])<<16) | ((in[3])<<24);
out_sz = ((in[4])<<0) | ((in[5])<<8) | ((in[6])<<16) | ((in[7])<<24);
if (in_sz != in_size-9)
return NULL;
out_buf = malloc(out_sz);
if (!out_buf)
return NULL;
//fprintf(stderr, "out_sz=%d\n", out_sz);
// Precompute reverse lookup of frequency.
rle = x = 0;
j = *cp++;
do {
if ((D.fc[j].F = *cp++) >= 128) {
D.fc[j].F &= ~128;
D.fc[j].F = ((D.fc[j].F & 127) << 8) | *cp++;
}
D.fc[j].C = x;
RansDecSymbolInit(&syms[j], D.fc[j].C, D.fc[j].F);
/* Build reverse lookup table */
if (!D.R) D.R = (unsigned char *)malloc(TOTFREQ);
memset(&D.R[x], j, D.fc[j].F);
x += D.fc[j].F;
if (!rle && j+1 == *cp) {
j = *cp++;
rle = *cp++;
} else if (rle) {
rle--;
j++;
} else {
j = *cp++;
}
} while(j);
assert(x < TOTFREQ);
RansState rans0, rans1, rans2, rans3;
uint8_t *ptr = cp;
RansDecInit(&rans0, &ptr);
RansDecInit(&rans1, &ptr);
RansDecInit(&rans2, &ptr);
RansDecInit(&rans3, &ptr);
int out_end = (out_sz&~3);
RansState R[4];
R[0] = rans0;
R[1] = rans1;
R[2] = rans2;
R[3] = rans3;
uint32_t mask = (1u << TF_SHIFT)-1;
for (i=0; i < out_end; i+=4) {
uint32_t m[4] = {R[0] & mask,
R[1] & mask,
R[2] & mask,
R[3] & mask};
uint8_t c[4] = {D.R[m[0]],
D.R[m[1]],
D.R[m[2]],
D.R[m[3]]};
out_buf[i+0] = c[0];
out_buf[i+1] = c[1];
out_buf[i+2] = c[2];
out_buf[i+3] = c[3];
// RansDecAdvanceSymbolStep(&R[0], &syms[c[0]], TF_SHIFT);
// RansDecAdvanceSymbolStep(&R[1], &syms[c[1]], TF_SHIFT);
// RansDecAdvanceSymbolStep(&R[2], &syms[c[2]], TF_SHIFT);
// RansDecAdvanceSymbolStep(&R[3], &syms[c[3]], TF_SHIFT);
R[0] = syms[c[0]].freq * (R[0]>>TF_SHIFT);
R[1] = syms[c[1]].freq * (R[1]>>TF_SHIFT);
R[2] = syms[c[2]].freq * (R[2]>>TF_SHIFT);
R[3] = syms[c[3]].freq * (R[3]>>TF_SHIFT);
R[0] += m[0] - syms[c[0]].start;
R[1] += m[1] - syms[c[1]].start;
R[2] += m[2] - syms[c[2]].start;
R[3] += m[3] - syms[c[3]].start;
RansDecRenorm(&R[0], &ptr);
RansDecRenorm(&R[1], &ptr);
RansDecRenorm(&R[2], &ptr);
RansDecRenorm(&R[3], &ptr);
}
rans0 = R[0];
rans1 = R[1];
rans2 = R[2];
rans3 = R[3];
switch(out_sz&3) {
unsigned char c;
case 0:
break;
case 1:
c = D.R[RansDecGet(&rans0, TF_SHIFT)];
RansDecAdvanceSymbol(&rans0, &ptr, &syms[c], TF_SHIFT);
out_buf[out_end] = c;
break;
case 2:
c = D.R[RansDecGet(&rans0, TF_SHIFT)];
RansDecAdvanceSymbol(&rans0, &ptr, &syms[c], TF_SHIFT);
out_buf[out_end] = c;
c = D.R[RansDecGet(&rans1, TF_SHIFT)];
RansDecAdvanceSymbol(&rans1, &ptr, &syms[c], TF_SHIFT);
out_buf[out_end+1] = c;
break;
case 3:
c = D.R[RansDecGet(&rans0, TF_SHIFT)];
RansDecAdvanceSymbol(&rans0, &ptr, &syms[c], TF_SHIFT);
out_buf[out_end] = c;
c = D.R[RansDecGet(&rans1, TF_SHIFT)];
RansDecAdvanceSymbol(&rans1, &ptr, &syms[c], TF_SHIFT);
out_buf[out_end+1] = c;
c = D.R[RansDecGet(&rans2, TF_SHIFT)];
RansDecAdvanceSymbol(&rans2, &ptr, &syms[c], TF_SHIFT);
out_buf[out_end+2] = c;
break;
}
*out_size = out_sz;
if (D.R) free(D.R);
return (unsigned char *)out_buf;
}
unsigned char *rans_compress_O1(unsigned char *in, unsigned int in_size,
unsigned int *out_size) {
unsigned char *out_buf = NULL, *out_end, *cp;
unsigned int last_i, tab_size, rle_i, rle_j;
RansEncSymbol (*syms)[256] = NULL; /* syms[256][256] */
int (*F)[256] = NULL; /* F[256][256] */
int *T = NULL; /* T[256] */
int i, j;
unsigned char c;
if (in_size < 4)
return rans_compress_O0(in, in_size, out_size);
syms = malloc(256 * sizeof(*syms));
if (!syms) goto cleanup;
F = calloc(256, sizeof(*F));
if (!F) goto cleanup;
T = calloc(256, sizeof(*T));
if (!T) goto cleanup;
out_buf = malloc(1.05*in_size + 257*257*3 + 9);
if (!out_buf) goto cleanup;
out_end = out_buf + (int)(1.05*in_size) + 257*257*3 + 9;
cp = out_buf+9;
//for (last = 0, i=in_size-1; i>=0; i--) {
// F[last][c = in[i]]++;
// T[last]++;
// last = c;
//}
for (last_i=i=0; i<in_size; i++) {
F[last_i][c = in[i]]++;
T[last_i]++;
last_i = c;
}
F[0][in[1*(in_size>>2)]]++;
F[0][in[2*(in_size>>2)]]++;
F[0][in[3*(in_size>>2)]]++;
T[0]+=3;
// Normalise so T[i] == TOTFREQ
for (rle_i = i = 0; i < 256; i++) {
int t2, m, M;
unsigned int x;
if (T[i] == 0)
continue;
//uint64_t p = (TOTFREQ * TOTFREQ) / t;
double p = ((double)TOTFREQ)/T[i];
for (t2 = m = M = j = 0; j < 256; j++) {
if (!F[i][j])
continue;
if (m < F[i][j])
m = F[i][j], M = j;
//if ((F[i][j] = (F[i][j] * p) / TOTFREQ) == 0)
if ((F[i][j] *= p) == 0)
F[i][j] = 1;
t2 += F[i][j];
}
t2++;
if (t2 < TOTFREQ)
F[i][M] += TOTFREQ-t2;
else
F[i][M] -= t2-TOTFREQ;
// Store frequency table
// i
if (rle_i) {
rle_i--;
} else {
*cp++ = i;
// FIXME: could use order-0 statistics to observe which alphabet
// symbols are present and base RLE on that ordering instead.
if (i && T[i-1]) {
for(rle_i=i+1; rle_i<256 && T[rle_i]; rle_i++)
;
rle_i -= i+1;
*cp++ = rle_i;
}
}
int *F_i_ = F[i];
x = 0;
rle_j = 0;
for (j = 0; j < 256; j++) {
if (F_i_[j]) {
//fprintf(stderr, "F[%d][%d]=%d, x=%d\n", i, j, F_i_[j], x);
// j
if (rle_j) {
rle_j--;
} else {
*cp++ = j;
if (!rle_j && j && F_i_[j-1]) {
for(rle_j=j+1; rle_j<256 && F_i_[rle_j]; rle_j++)
;
rle_j -= j+1;
*cp++ = rle_j;
}
}
// F_i_[j]
if (F_i_[j]<128) {
*cp++ = F_i_[j];
} else {
*cp++ = 128 | (F_i_[j]>>8);
*cp++ = F_i_[j]&0xff;
}
RansEncSymbolInit(&syms[i][j], x, F_i_[j], TF_SHIFT);
x += F_i_[j];
}
}
*cp++ = 0;
}
*cp++ = 0;
//write(1, out_buf+4, cp-(out_buf+4));
tab_size = cp - out_buf;
assert(tab_size < 257*257*3);
RansState rans0, rans1, rans2, rans3;
RansEncInit(&rans0);
RansEncInit(&rans1);
RansEncInit(&rans2);
RansEncInit(&rans3);
uint8_t* ptr = out_end;
int isz4 = in_size>>2;
int i0 = 1*isz4-2;
int i1 = 2*isz4-2;
int i2 = 3*isz4-2;
int i3 = 4*isz4-2;
unsigned char l0 = in[i0+1];
unsigned char l1 = in[i1+1];
unsigned char l2 = in[i2+1];
unsigned char l3 = in[i3+1];
// Deal with the remainder
l3 = in[in_size-1];
for (i3 = in_size-2; i3 > 4*isz4-2; i3--) {
unsigned char c3 = in[i3];
RansEncPutSymbol(&rans3, &ptr, &syms[c3][l3]);
l3 = c3;
}
for (; i0 >= 0; i0--, i1--, i2--, i3--) {
unsigned char c0, c1, c2, c3;
RansEncSymbol *s3 = &syms[c3 = in[i3]][l3];
RansEncSymbol *s2 = &syms[c2 = in[i2]][l2];
RansEncSymbol *s1 = &syms[c1 = in[i1]][l1];
RansEncSymbol *s0 = &syms[c0 = in[i0]][l0];
RansEncPutSymbol(&rans3, &ptr, s3);
RansEncPutSymbol(&rans2, &ptr, s2);
RansEncPutSymbol(&rans1, &ptr, s1);
RansEncPutSymbol(&rans0, &ptr, s0);
l0 = c0;
l1 = c1;
l2 = c2;
l3 = c3;
}
RansEncPutSymbol(&rans3, &ptr, &syms[0][l3]);
RansEncPutSymbol(&rans2, &ptr, &syms[0][l2]);
RansEncPutSymbol(&rans1, &ptr, &syms[0][l1]);
RansEncPutSymbol(&rans0, &ptr, &syms[0][l0]);
RansEncFlush(&rans3, &ptr);
RansEncFlush(&rans2, &ptr);
RansEncFlush(&rans1, &ptr);
RansEncFlush(&rans0, &ptr);
*out_size = (out_end - ptr) + tab_size;
cp = out_buf;
*cp++ = 1; // order
*cp++ = ((*out_size-9)>> 0) & 0xff;
*cp++ = ((*out_size-9)>> 8) & 0xff;
*cp++ = ((*out_size-9)>>16) & 0xff;
*cp++ = ((*out_size-9)>>24) & 0xff;
*cp++ = (in_size>> 0) & 0xff;
*cp++ = (in_size>> 8) & 0xff;
*cp++ = (in_size>>16) & 0xff;
*cp++ = (in_size>>24) & 0xff;
memmove(out_buf + tab_size, ptr, out_end-ptr);
cleanup:
free(syms);
free(F);
free(T);
return out_buf;
}
unsigned char *rans_uncompress_O1(unsigned char *in, unsigned int in_size,
unsigned int *out_size) {
/* Load in the static tables */
unsigned char *cp = in + 9;
int i, j = -999, x, out_sz, in_sz, rle_i, rle_j;
char *out_buf = NULL;
ari_decoder *D = NULL; /* D[256] */
RansDecSymbol (*syms)[256] = NULL; /* syms[256][256] */
if (*in++ != 1) // Order-1 check
return NULL;
in_sz = ((in[0])<<0) | ((in[1])<<8) | ((in[2])<<16) | ((in[3])<<24);
out_sz = ((in[4])<<0) | ((in[5])<<8) | ((in[6])<<16) | ((in[7])<<24);
if (in_sz != in_size-9)
return NULL;
D = calloc(256, sizeof(*D));
if (!D) goto cleanup;
syms = malloc(256 * sizeof(*syms));
if (!syms) goto cleanup;
//fprintf(stderr, "out_sz=%d\n", out_sz);
//i = *cp++;
rle_i = 0;
i = *cp++;
do {
rle_j = x = 0;
j = *cp++;
do {
if ((D[i].fc[j].F = *cp++) >= 128) {
D[i].fc[j].F &= ~128;
D[i].fc[j].F = ((D[i].fc[j].F & 127) << 8) | *cp++;
}
D[i].fc[j].C = x;
//fprintf(stderr, "i=%d j=%d F=%d C=%d\n", i, j, D[i].fc[j].F, D[i].fc[j].C);
if (!D[i].fc[j].F)
D[i].fc[j].F = TOTFREQ;
RansDecSymbolInit(&syms[i][j], D[i].fc[j].C, D[i].fc[j].F);
/* Build reverse lookup table */
if (!D[i].R) {
D[i].R = (unsigned char *)malloc(TOTFREQ);
if (!D[i].R)
goto cleanup;
}
memset(&D[i].R[x], j, D[i].fc[j].F);
x += D[i].fc[j].F;
assert(x <= TOTFREQ);
if (!rle_j && j+1 == *cp) {
j = *cp++;
rle_j = *cp++;
} else if (rle_j) {
rle_j--;
j++;
} else {
j = *cp++;
}
} while(j);
if (!rle_i && i+1 == *cp) {
i = *cp++;
rle_i = *cp++;
} else if (rle_i) {
rle_i--;
i++;
} else {
i = *cp++;
}
} while (i);
// Precompute reverse lookup of frequency.
RansState rans0, rans1, rans2, rans3;
uint8_t *ptr = cp;
RansDecInit(&rans0, &ptr);
RansDecInit(&rans1, &ptr);
RansDecInit(&rans2, &ptr);
RansDecInit(&rans3, &ptr);
int isz4 = out_sz>>2;
int l0 = 0;
int l1 = 0;
int l2 = 0;
int l3 = 0;
int i4[] = {0*isz4, 1*isz4, 2*isz4, 3*isz4};
RansState R[4];
R[0] = rans0;
R[1] = rans1;
R[2] = rans2;
R[3] = rans3;
/* Allocate output buffer */
out_buf = malloc(out_sz);
if (!out_buf) goto cleanup;
for (; i4[0] < isz4; i4[0]++, i4[1]++, i4[2]++, i4[3]++) {
uint32_t m[4] = {R[0] & ((1u << TF_SHIFT)-1),
R[1] & ((1u << TF_SHIFT)-1),
R[2] & ((1u << TF_SHIFT)-1),
R[3] & ((1u << TF_SHIFT)-1)};
uint8_t c[4] = {D[l0].R[m[0]],
D[l1].R[m[1]],
D[l2].R[m[2]],
D[l3].R[m[3]]};
out_buf[i4[0]] = c[0];
out_buf[i4[1]] = c[1];
out_buf[i4[2]] = c[2];
out_buf[i4[3]] = c[3];
//RansDecAdvanceSymbolStep(&R[0], &syms[l0][c[0]], TF_SHIFT);
//RansDecAdvanceSymbolStep(&R[1], &syms[l1][c[1]], TF_SHIFT);
//RansDecAdvanceSymbolStep(&R[2], &syms[l2][c[2]], TF_SHIFT);
//RansDecAdvanceSymbolStep(&R[3], &syms[l3][c[3]], TF_SHIFT);
R[0] = syms[l0][c[0]].freq * (R[0]>>TF_SHIFT);
R[1] = syms[l1][c[1]].freq * (R[1]>>TF_SHIFT);
R[2] = syms[l2][c[2]].freq * (R[2]>>TF_SHIFT);
R[3] = syms[l3][c[3]].freq * (R[3]>>TF_SHIFT);
R[0] += m[0] - syms[l0][c[0]].start;
R[1] += m[1] - syms[l1][c[1]].start;
R[2] += m[2] - syms[l2][c[2]].start;
R[3] += m[3] - syms[l3][c[3]].start;
RansDecRenorm(&R[0], &ptr);
RansDecRenorm(&R[1], &ptr);
RansDecRenorm(&R[2], &ptr);
RansDecRenorm(&R[3], &ptr);
l0 = c[0];
l1 = c[1];
l2 = c[2];
l3 = c[3];
}
rans0 = R[0];
rans1 = R[1];
rans2 = R[2];
rans3 = R[3];
// Remainder
for (; i4[3] < out_sz; i4[3]++) {
unsigned char c3 = D[l3].R[RansDecGet(&rans3, TF_SHIFT)];
out_buf[i4[3]] = c3;
RansDecAdvanceSymbol(&rans3, &ptr, &syms[l3][c3], TF_SHIFT);
l3 = c3;
}
*out_size = out_sz;
cleanup:
if (D) {
for (i = 0; i < 256; i++)
if (D[i].R) free(D[i].R);
free(D);
}
free(syms);
return (unsigned char *)out_buf;
}
/*-----------------------------------------------------------------------------
* Simple interface to the order-0 vs order-1 encoders and decoders.
*/
unsigned char *rans_compress(unsigned char *in, unsigned int in_size,
unsigned int *out_size, int order) {
return order
? rans_compress_O1(in, in_size, out_size)
: rans_compress_O0(in, in_size, out_size);
}
unsigned char *rans_uncompress(unsigned char *in, unsigned int in_size,
unsigned int *out_size) {
/* Both rans_uncompress functions need to be able to read at least 9
bytes. */
if (in_size < 9)
return NULL;
return in[0]
? rans_uncompress_O1(in, in_size, out_size)
: rans_uncompress_O0(in, in_size, out_size);
}
#ifdef TEST_MAIN
/*-----------------------------------------------------------------------------
* Main.
*
* This is a simple command line tool for testing order-0 and order-1
* compression using the rANS codec. Simply compile with
*
* gcc -DTEST_MAIN -O3 -I. cram/rANS_static.c -o cram/rANS_static
*
* Usage: cram/rANS_static -o0 < file > file.o0
* cram/rANS_static -d < file.o0 > file2
*
* cram/rANS_static -o1 < file > file.o1
* cram/rANS_static -d < file.o1 > file2
*/
int main(int argc, char **argv) {
int opt, order = 0;
unsigned char in_buf[BLK_SIZE2+257*257*3];
int decode = 0;
FILE *infp = stdin, *outfp = stdout;
struct timeval tv1, tv2;
size_t bytes = 0;
extern char *optarg;
extern int optind;
while ((opt = getopt(argc, argv, "o:d")) != -1) {
switch (opt) {
case 'o':
order = atoi(optarg);
break;
case 'd':
decode = 1;
break;
}
}
order = order ? 1 : 0; // Only support O(0) and O(1)
if (optind < argc) {
if (!(infp = fopen(argv[optind], "rb"))) {
perror(argv[optind]);
return 1;
}
optind++;
}
if (optind < argc) {
if (!(outfp = fopen(argv[optind], "wb"))) {
perror(argv[optind]);
return 1;
}
optind++;
}
gettimeofday(&tv1, NULL);
if (decode) {
// Only used in some test implementations of RC_GetFreq()
//RC_init();
//RC_init2();
for (;;) {
uint32_t in_size, out_size;
unsigned char *out;
if (9 != fread(in_buf, 1, 9, infp))
break;
in_size = *(int *)&in_buf[1];
if (in_size != fread(in_buf+9, 1, in_size, infp)) {
fprintf(stderr, "Truncated input\n");
exit(1);
}
out = rans_uncompress(in_buf, in_size+9, &out_size);
if (!out)
abort();
fwrite(out, 1, out_size, outfp);
free(out);
bytes += out_size;
}
} else {
for (;;) {
uint32_t in_size, out_size;
unsigned char *out;
in_size = fread(in_buf, 1, BLK_SIZE, infp);
if (in_size <= 0)
break;
out = rans_compress(in_buf, in_size, &out_size, order);
fwrite(out, 1, out_size, outfp);
free(out);
bytes += in_size;
}
}
gettimeofday(&tv2, NULL);
fprintf(stderr, "Took %ld microseconds, %5.1f MB/s\n",
(long)(tv2.tv_sec - tv1.tv_sec)*1000000 +
tv2.tv_usec - tv1.tv_usec,
(double)bytes / ((long)(tv2.tv_sec - tv1.tv_sec)*1000000 +
tv2.tv_usec - tv1.tv_usec));
return 0;
}
#endif