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rle.c
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rle.c
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#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
}
}