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#include <u.h>
#include <libn.h>
#include <libn/macro/qsort.h>
#include <libbio.h>
// -----------------------------------------------------------------------
// globals
uint64 aln·shft = (2ULL * (aln·K - 1ULL));
uint64 aln·mask = (1ULL << (2*aln·K)) - 1ULL;
// -----------------------------------------------------------------------
// static data
static uint64 nuctab[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
};
// -----------------------------------------------------------------------
// hash functions
enum
{
MURM641 = 0xff51afd7ed558ccd,
MURM642 = 0xc4ceb9fe1a85ec53
};
static
uint64
minihash(uint64 x, uint64 mask)
{
x = (~x + (x << 21)) & mask;
x = x ^ (x >> 24);
x = (x + (x << 3) + (x << 8)) & mask;
x = x ^ (x >> 14);
x = (x + (x << 2) + (x << 4)) & mask;
x = x ^ (x >> 28);
x = (x + (x << 31));
return x;
}
static
uint64
murmurhash(uint64 x, uint64 mask)
{
x = x ^ (x >> 33);
x = (x * MURM641);
x = x ^ (x >> 33);
x = (x * MURM642);
x = x ^ (x >> 33);
return x;
}
// -----------------------------------------------------------------------
// locality sensitive hashing (with spatial extent)
static
void
sortpos(uintptr len, uint64 vals[], int locs[])
{
int tmpi;
uint64 tmpu64;
#define LESS(i, j) (locs[i] < locs[j])
#define SWAP(i, j) (tmpu64 = vals[i], tmpi = locs[i], \
vals[i] = vals[j], locs[i] = locs[j], \
vals[j] = tmpu64 , locs[j] = tmpi)
QSORT(len, LESS, SWAP);
#undef LESS
#undef SWAP
}
/*
* sketch
* @param seq: '0' terminated string
* @param len: number of sequential sketches to keep
* @param vals: buffer to store hashes of sketch.
* @param locs: buffer to store location of sketch hashes
*/
error
aln·sketch(byte *seq, int len, uint64 *vals[aln·N], int *locs[aln·N])
{
int i, n, l, *loc;
uint64 kmer, h[3], *val;
int tmpi[2];
uint64 tmpu[2];
for(n = 0; n < aln·N; n++) {
for(l = 0; l < len; l++) {
vals[n][l] = UINT64_MAX;
}
}
kmer = UINT64_MAX;
for(l = 0; *seq != '\0'; seq++, l++) {
kmer = ((kmer << 2) | nuctab[*seq]) & aln·mask;
h[0] = minihash(kmer, aln·mask);
h[1] = murmurhash(kmer, aln·mask);
for(n = 0; n < aln·N; n++) {
val = vals[n];
loc = locs[n];
h[2] = (h[0] + n * h[1]) & aln·mask;
for (i = 0; i < len && h[2] < val[i]; i++) {
;
}
tmpu[1] = h[2];
tmpi[1] = l;
for(i -= 1; i >= 0; i--) {
tmpu[0] = tmpu[1], tmpu[1] = val[i], val[i] = tmpu[0];
tmpi[0] = tmpi[1], tmpi[1] = loc[i], loc[i] = tmpi[0];
}
}
}
for(n = 0; n < aln·N; n++) {
sortpos(len, vals[n], locs[n]);
}
return 0;
}
static
int
lessarrs(int len, uint64 a[], uint64 b[])
{
int l;
for(l = 0; l < len; l++) {
if (a[l] < b[l]) return 1;
if (a[l] > b[l]) return 0;
}
return 0;
}
static
void
swaparrs(int len, uint64 a[], uint64 b[])
{
int l;
uint64 tmp;
for(l = 0; l < len; l++) {
tmp = a[l], a[l] = b[l], b[l] = tmp;
}
}
error
aln·sort(uintptr n, int len, uint64 *vals)
{
#define LESS(i, j) (lessarrs(len, vals+((i)*len), vals+((j)*len)))
#define SWAP(i, j) (swaparrs(len, vals+((i)*len), vals+((j)*len)))
QSORT(n, LESS, SWAP);
#undef LESS
#undef SWAP
return 0;
}
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