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
|
#include <string.h>
#include <assert.h>
#include <stdlib.h>
#include <stdio.h>
#include "rle.h"
const uint8_t rle_auxtab[8] = { 0x01, 0x11, 0x21, 0x31, 0x03, 0x13, 0x07, 0x17 };
// insert symbol $a after $x symbols in $str; marginal counts added to $cnt; returns the size increase
int rle_insert_cached(uint8_t *block, int64_t x, int a, int64_t rl, int64_t cnt[6], const int64_t ec[6], int *beg, int64_t bc[6])
{
uint16_t *nptr = (uint16_t*)block;
int diff;
block += 2; // skip the first 2 counting bytes
if (*nptr == 0) {
memset(cnt, 0, 48);
diff = rle_enc1(block, a, rl);
} else {
uint8_t *p, *end = block + *nptr, *q;
int64_t pre, z, l = 0, tot, beg_l;
int c = -1, n_bytes = 0, n_bytes2, t = 0;
uint8_t tmp[24];
beg_l = bc[0] + bc[1] + bc[2] + bc[3] + bc[4] + bc[5];
tot = ec[0] + ec[1] + ec[2] + ec[3] + ec[4] + ec[5];
if (x < beg_l) {
beg_l = 0, *beg = 0;
memset(bc, 0, 48);
}
if (x == beg_l) {
p = q = block + (*beg); z = beg_l;
memcpy(cnt, bc, 48);
} else if (x - beg_l <= ((tot-beg_l)>>1) + ((tot-beg_l)>>3)) { // forward
z = beg_l; p = block + (*beg);
memcpy(cnt, bc, 48);
while (z < x) {
rle_dec1(p, c, l);
z += l; cnt[c] += l;
}
for (q = p - 1; *q>>6 == 2; --q);
} else { // backward
memcpy(cnt, ec, 48);
z = tot; p = end;
while (z >= x) {
--p;
if (*p>>6 != 2) {
l |= *p>>7? (int64_t)rle_auxtab[*p>>3&7]>>4 << t : *p>>3;
z -= l; cnt[*p&7] -= l;
l = 0; t = 0;
} else {
l |= (*p&0x3fL) << t;
t += 6;
}
}
q = p;
rle_dec1(p, c, l);
z += l; cnt[c] += l;
}
*beg = q - block;
memcpy(bc, cnt, 48);
bc[c] -= l;
n_bytes = p - q;
if (x == z && a != c && p < end) { // then try the next run
int tc;
int64_t tl;
q = p;
rle_dec1(q, tc, tl);
if (a == tc)
c = tc, n_bytes = q - p, l = tl, z += l, p = q, cnt[tc] += tl;
}
if (z != x) cnt[c] -= z - x;
pre = x - (z - l); p -= n_bytes;
if (a == c) { // insert to the same run
n_bytes2 = rle_enc1(tmp, c, l + rl);
} else if (x == z) { // at the end; append to the existing run
p += n_bytes; n_bytes = 0;
n_bytes2 = rle_enc1(tmp, a, rl);
} else { // break the current run
n_bytes2 = rle_enc1(tmp, c, pre);
n_bytes2 += rle_enc1(tmp + n_bytes2, a, rl);
n_bytes2 += rle_enc1(tmp + n_bytes2, c, l - pre);
}
if (n_bytes != n_bytes2 && end != p + n_bytes) // size changed
memmove(p + n_bytes2, p + n_bytes, end - p - n_bytes);
memcpy(p, tmp, n_bytes2);
diff = n_bytes2 - n_bytes;
}
return (*nptr += diff);
}
int rle_insert(uint8_t *block, int64_t x, int a, int64_t rl, int64_t cnt[6], const int64_t ec[6])
{
int beg = 0;
int64_t bc[6];
memset(bc, 0, 48);
return rle_insert_cached(block, x, a, rl, cnt, ec, &beg, bc);
}
void rle_split(uint8_t *block, uint8_t *new_block)
{
int n = *(uint16_t*)block;
uint8_t *end = block + 2 + n, *q = block + 2 + (n>>1);
while (*q>>6 == 2) --q;
memcpy(new_block + 2, q, end - q);
*(uint16_t*)new_block = end - q;
*(uint16_t*)block = q - block - 2;
}
void rle_count(const uint8_t *block, int64_t cnt[6])
{
const uint8_t *q = block + 2, *end = q + *(uint16_t*)block;
while (q < end) {
int c;
int64_t l;
rle_dec1(q, c, l);
cnt[c] += l;
}
}
void rle_print(const uint8_t *block, int expand)
{
const uint16_t *p = (const uint16_t*)block;
const uint8_t *q = block + 2, *end = block + 2 + *p;
while (q < end) {
int c;
int64_t l, x;
rle_dec1(q, c, l);
if (expand) for (x = 0; x < l; ++x) putchar("$ACGTN"[c]);
else printf("%c%ld", "$ACGTN"[c], (long)l);
}
putchar('\n');
}
void rle_rank2a(const uint8_t *block, int64_t x, int64_t y, int64_t *cx, int64_t *cy, const int64_t ec[6])
{
int a;
int64_t tot, cnt[6];
const uint8_t *p;
y = y >= x? y : x;
tot = ec[0] + ec[1] + ec[2] + ec[3] + ec[4] + ec[5];
if (tot == 0) return;
if (x <= (tot - y) + (tot>>3)) {
int c = 0;
int64_t l, z = 0;
memset(cnt, 0, 48);
p = block + 2;
while (z < x) {
rle_dec1(p, c, l);
z += l; cnt[c] += l;
}
for (a = 0; a != 6; ++a) cx[a] += cnt[a];
cx[c] -= z - x;
if (cy) {
while (z < y) {
rle_dec1(p, c, l);
z += l; cnt[c] += l;
}
for (a = 0; a != 6; ++a) cy[a] += cnt[a];
cy[c] -= z - y;
}
} else {
#define move_backward(_x) \
while (z >= (_x)) { \
--p; \
if (*p>>6 != 2) { \
l |= *p>>7? (int64_t)rle_auxtab[*p>>3&7]>>4 << t : *p>>3; \
z -= l; cnt[*p&7] -= l; \
l = 0; t = 0; \
} else { \
l |= (*p&0x3fL) << t; \
t += 6; \
} \
} \
int t = 0;
int64_t l = 0, z = tot;
memcpy(cnt, ec, 48);
p = block + 2 + *(const uint16_t*)block;
if (cy) {
move_backward(y)
for (a = 0; a != 6; ++a) cy[a] += cnt[a];
cy[*p&7] += y - z;
}
move_backward(x)
for (a = 0; a != 6; ++a) cx[a] += cnt[a];
cx[*p&7] += x - z;
#undef move_backward
}
}
|