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Homopolymer-compressed k-mer sketch

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This commit is contained in:
Heng Li
2017-04-06 15:37:34 -04:00
parent 2bb0839177
commit 01baa847a1
8 changed files with 838 additions and 14 deletions
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sketch.c
+55 -14
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@@ -36,67 +36,108 @@ static inline uint64_t hash64(uint64_t key, uint64_t mask)
return key;
}
typedef struct { // a simplified version of kdq
int front, count;
int a[32];
} tiny_queue_t;
static inline void tq_push(tiny_queue_t *q, int x)
{
q->a[((q->count++) + q->front) & 0x1f] = x;
}
static inline int tq_shift(tiny_queue_t *q)
{
int x;
if (q->count == 0) return -1;
x = q->a[q->front++];
q->front &= 0x1f;
--q->count;
return x;
}
/**
* Find symmetric (w,k)-minimizers on a DNA sequence
*
* @param km thread-local memory pool; using NULL falls back to malloc()
* @param str DNA sequence
* @param len length of $str
* @param w find a minimizer for every $w consecutive k-mers
* @param k k-mer size
* @param rid reference ID; will be copied to the output $p array
* @param p minimizers; p->a[i].x is the 2k-bit hash value;
* @param is_hpc homopolymer-compressed or not
* @param p minimizers
* p->a[i].x = kMer<<8 | kmerSpan
* p->a[i].y = rid<<32 | lastPos<<1 | strand
* where lastPos is the position of the last base of the i-th minimizer,
* and strand indicates whether the minimizer comes from the top or the bottom strand.
* Callers may want to set "p->n = 0"; otherwise results are appended to p
*/
void mm_sketch(const char *str, int len, int w, int k, uint32_t rid, mm128_v *p)
void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, int is_hpc, mm128_v *p)
{
uint64_t shift1 = 2 * (k - 1), mask = (1ULL<<2*k) - 1, kmer[2] = {0,0};
int i, j, l, buf_pos, min_pos;
int i, j, l, buf_pos, min_pos, kmer_span = 0;
mm128_t *buf, min = { UINT64_MAX, UINT64_MAX };
tiny_queue_t tq;
assert(len > 0 && w > 0 && k > 0);
assert(len > 0 && w > 0 && k > 0 && k <= 28); // 56 bits for k-mer; could use long k-mers, but 28 enough in practice
buf = (mm128_t*)alloca(w * 16);
memset(buf, 0xff, w * 16);
memset(&tq, 0, sizeof(tiny_queue_t));
kv_resize(mm128_t, km, *p, p->n + len/w);
for (i = l = buf_pos = min_pos = 0; i < len; ++i) {
int c = seq_nt4_table[(uint8_t)str[i]];
mm128_t info = { UINT64_MAX, UINT64_MAX };
if (c < 4) { // not an ambiguous base
int z;
if (is_hpc) {
int skip_len = 1;
if (i + 1 < len && seq_nt4_table[(uint8_t)str[i + 1]] == c) {
for (skip_len = 2; i + skip_len < len; ++skip_len)
if (seq_nt4_table[(uint8_t)str[i + skip_len]] != c)
break;
i += skip_len - 1; // put $i at the end of the current homopolymer run
}
tq_push(&tq, skip_len);
kmer_span += skip_len;
if (tq.count > k) kmer_span -= tq_shift(&tq);
if (kmer_span >= 256) continue; // make sure $kmer_span does not take more than 8 bits
} else kmer_span = l + 1 < k? l + 1 : k;
kmer[0] = (kmer[0] << 2 | c) & mask; // forward k-mer
kmer[1] = (kmer[1] >> 2) | (3ULL^c) << shift1; // reverse k-mer
if (kmer[0] == kmer[1]) continue; // skip "symmetric k-mers" as we don't know it strand
z = kmer[0] < kmer[1]? 0 : 1; // strand
if (++l >= k)
info.x = hash64(kmer[z], mask), info.y = (uint64_t)rid<<32 | (uint32_t)i<<1 | z;
} else l = 0;
if (++l >= k) {
info.x = hash64(kmer[z], mask) << 8 | kmer_span;
info.y = (uint64_t)rid<<32 | (uint32_t)i<<1 | z;
}
} else l = 0, tq.count = tq.front = 0;
buf[buf_pos] = info; // need to do this here as appropriate buf_pos and buf[buf_pos] are needed below
if (l == w + k - 1) { // special case for the first window - because identical k-mers are not stored yet
for (j = buf_pos + 1; j < w; ++j)
if (min.x == buf[j].x && buf[j].y != min.y) kv_push(mm128_t, *p, buf[j]);
if (min.x == buf[j].x && buf[j].y != min.y) kv_push(mm128_t, km, *p, buf[j]);
for (j = 0; j < buf_pos; ++j)
if (min.x == buf[j].x && buf[j].y != min.y) kv_push(mm128_t, *p, buf[j]);
if (min.x == buf[j].x && buf[j].y != min.y) kv_push(mm128_t, km, *p, buf[j]);
}
if (info.x <= min.x) { // a new minimum; then write the old min
if (l >= w + k) kv_push(mm128_t, *p, min);
if (l >= w + k) kv_push(mm128_t, km, *p, min);
min = info, min_pos = buf_pos;
} else if (buf_pos == min_pos) { // old min has moved outside the window
if (l >= w + k - 1) kv_push(mm128_t, *p, min);
if (l >= w + k - 1) kv_push(mm128_t, km, *p, min);
for (j = buf_pos + 1, min.x = UINT64_MAX; j < w; ++j) // the two loops are necessary when there are identical k-mers
if (min.x >= buf[j].x) min = buf[j], min_pos = j; // >= is important s.t. min is always the closest k-mer
for (j = 0; j <= buf_pos; ++j)
if (min.x >= buf[j].x) min = buf[j], min_pos = j;
if (l >= w + k - 1) { // write identical k-mers
for (j = buf_pos + 1; j < w; ++j) // these two loops make sure the output is sorted
if (min.x == buf[j].x && min.y != buf[j].y) kv_push(mm128_t, *p, buf[j]);
if (min.x == buf[j].x && min.y != buf[j].y) kv_push(mm128_t, km, *p, buf[j]);
for (j = 0; j <= buf_pos; ++j)
if (min.x == buf[j].x && min.y != buf[j].y) kv_push(mm128_t, *p, buf[j]);
if (min.x == buf[j].x && min.y != buf[j].y) kv_push(mm128_t, km, *p, buf[j]);
}
}
if (++buf_pos == w) buf_pos = 0;
}
if (min.x != UINT64_MAX)
kv_push(mm128_t, *p, min);
kv_push(mm128_t, km, *p, min);
}