-
Notifications
You must be signed in to change notification settings - Fork 555
/
rle.c
191 lines (180 loc) · 4.71 KB
/
rle.c
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
}
}