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match.c
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match.c
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#include <stdlib.h>
#include <unistd.h>
#include <string.h>
#include <stdarg.h>
#include <stdio.h>
#include <zlib.h>
#include "fermi2.h"
#include "kvec.h"
#include "kstring.h"
#include "kseq.h"
KSEQ_DECLARE(gzFile)
int kvsprintf(kstring_t *s, const char *fmt, va_list ap)
{
va_list args;
int l;
va_copy(args, ap);
l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args); // This line does not work with glibc 2.0. See `man snprintf'.
va_end(args);
if (l + 1 > s->m - s->l) {
s->m = s->l + l + 2;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
va_copy(args, ap);
l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args);
va_end(args);
}
s->l += l;
return l;
}
int ksprintf(kstring_t *s, const char *fmt, ...)
{
va_list ap;
int l;
va_start(ap, fmt);
l = kvsprintf(s, fmt, ap);
va_end(ap);
return l;
}
int fmd_smem1_core(const rld_t *e, int min_occ, int len, const uint8_t *q, int x, fmdsmem_v *mem, rldintv_v *curr, rldintv_v *prev)
{ // for more comments, see bwa/bwt.c
int i, j, c, ret;
rldintv_t ik, ok[6];
rldintv_v *swap;
size_t oldn = mem->n;
fmd_set_intv(e, q[x], ik);
ik.info = x + 1;
if (ik.x[2] == 0) return x + 1;
for (i = x + 1, curr->n = 0; i < len; ++i) { // forward extension
c = fmd_comp(q[i]);
rld_extend(e, &ik, ok, 0);
if (ok[c].x[2] != ik.x[2]) {
kv_push(rldintv_t, *curr, ik);
if (ok[c].x[2] < min_occ) break;
}
ik = ok[c]; ik.info = i + 1;
}
if (i == len) kv_push(rldintv_t, *curr, ik);
kv_reverse(rldintv_t, *curr, 0);
ret = curr->a[0].info;
swap = curr; curr = prev; prev = swap;
for (i = x - 1; i >= -1; --i) {
c = i < 0? 0 : q[i];
for (j = 0, curr->n = 0; j < prev->n; ++j) {
rldintv_t *p = &prev->a[j];
rld_extend(e, p, ok, 1);
if (c == 0 || ok[c].x[2] < min_occ) {
if (curr->n == 0) {
if (mem->n == oldn || i + 1 < mem->a[mem->n-1].ik.info>>32) {
fmdsmem_t *q;
kv_pushp(fmdsmem_t, *mem, &q);
q->ik = *p; q->ik.info |= (uint64_t)(i + 1)<<32;
memcpy(q->ok[0], ok, 6 * sizeof(rldintv_t));
}
}
} else if (curr->n == 0 || ok[c].x[2] != curr->a[curr->n-1].x[2]) {
ok[c].info = p->info;
kv_push(rldintv_t, *curr, ok[c]);
}
}
if (curr->n == 0) break;
swap = curr; curr = prev; prev = swap;
}
kv_reverse(fmdsmem_t, *mem, oldn);
return ret;
}
int fmd_smem(const rld_t *e, const uint8_t *q, fmdsmem_v *mem, int min_occ, rldintv_v *curr, rldintv_v *prev)
{
int x = 0, len;
mem->n = 0;
len = strlen((char*)q);
do {
x = fmd_smem1_core(e, min_occ, len, q, x, mem, curr, prev);
} while (x < len);
return mem->n;
}
void fm_exact(const rld_t *e, const char *s, int64_t *_l, int64_t *_u)
{
extern unsigned char seq_nt6_table[128];
int64_t i, l = 0, u = e->mcnt[0];
for (i = strlen(s) - 1; i >= 0; --i) {
int c = (uint8_t)s[i];
c = c < 6? c : c < 128? seq_nt6_table[c] : 5;
l = e->cnt[c] + rld_rank11(e, l, c);
u = e->cnt[c] + rld_rank11(e, u, c);
if (l >= u) break;
}
*_l = l, *_u = u;
}
extern void seq_char2nt6(int l, unsigned char *s);
extern void seq_revcomp6(int l, unsigned char *s);
extern void kt_for(int n_threads, void (*func)(void*,long,int), void *data, long n);
typedef struct {
rldintv_v curr, prev;
fmdsmem_v smem;
kstring_t str, cmp[2];
} thrmem_t;
typedef struct {
const rld_t *e;
const fmsa_t *sa;
int max_sa_occ, min_occ, min_len;
int partial, discovery, kmer;
int n_threads;
thrmem_t *mem;
int n_seqs, m_seqs;
char **name, **seq, **qual, **out;
} global_t;
static void discover(const rld_t *e, const fmdsmem_t *q, const fmdsmem_t *p, int l_seq, const char *seq, const char *qual, kstring_t *s, kstring_t cmp[2])
{
int start, end, i, ext[2], left, right, tmp_l, pos;
int64_t occ[2];
rldintv_t ovlp;
// find the coordinate from which the extension will be applied
if (q == 0 && p == 0) {
start = 0; end = l_seq;
} else if (q == 0) {
if (p->ik.info>>32 == 0) return; // no novel allele
start = 0; end = p->ik.info>>32;
} else if (p == 0) {
if ((uint32_t)q->ik.info == l_seq) return; // no novel allele
start = (uint32_t)q->ik.info; end = l_seq;
} else {
start = (uint32_t)q->ik.info, end = p->ik.info>>32;
if (start >= end && q->ok[1][0].x[2] == q->ik.x[2] && p->ik.x[2] == p->ok[0][0].x[2]) return;
}
// find the SAI for the overlap (if applicable)
memset(&ovlp, 0, sizeof(rldintv_t));
ovlp.x[2] = e->mcnt[0];
if (start <= end) { // no overlap
left = start - 1, right = end;
for (i = left + 1; i < right; ++i)
if (seq[i] < 5) break;
if (i == end) return; // the gap is filled with "N"
} else {
rldintv_t ok[6];
left = end - 1, right = start;
for (i = right - 1; i > left; --i) {
rld_extend(e, &ovlp, ok, 1);
ovlp = ok[(int)seq[i]];
assert(ovlp.x[2] > 0);
}
}
occ[0] = occ[1] = 0;
ext[0] = ext[1] = 0;
// left extension
if (left >= 0) {
int64_t l = ovlp.x[0], u = l + ovlp.x[2];
uint64_t ol[6], ou[6];
for (i = left; i >= 0; --i) {
int c = seq[i];
rld_rank1a(e, l, ol);
rld_rank1a(e, u, ou);
l = e->cnt[c] + ol[c];
u = e->cnt[c] + ou[c];
if (u - l <= q->ik.x[2]) break;
}
assert(i >= 0 && u - l == q->ik.x[2]);
ext[0] = left + 1 - i;
occ[0] = u - l;
}
// right extension
if (right < l_seq) {
int64_t l = ovlp.x[1], u = l + ovlp.x[2];
uint64_t ol[6], ou[6];
for (i = right; i < l_seq; ++i) {
int c = fmd_comp(seq[i]);
rld_rank1a(e, l, ol);
rld_rank1a(e, u, ou);
l = e->cnt[c] + ol[c];
u = e->cnt[c] + ou[c];
if (u - l <= p->ik.x[2]) break;
}
assert(i < l_seq && u - l == p->ik.x[2]);
ext[1] = i + 1 - right;
occ[1] = u - l;
}
if (ovlp.x[2] == occ[0] + occ[1]) return;
// cut sequence
pos = left + 1 - ext[0];
cmp[0].l = cmp[1].l = 0;
kputsn(&seq[pos], (right + ext[1]) - (left + 1 - ext[0]), &cmp[0]);
kputsn(cmp[0].s, cmp[0].l, &cmp[1]);
seq_revcomp6(cmp[1].l, (uint8_t*)cmp[1].s);
// print
if (ovlp.x[2] == e->mcnt[0]) ovlp.x[2] = 0;
ksprintf(s, "NS\t%d\t", pos);
tmp_l = end < start? start - end : 0;
if (strcmp(cmp[0].s, cmp[1].s) <= 0) {
ksprintf(s, "+\t%d\t%d\t%d\t%ld\t%ld\t%ld\t", ext[0] + tmp_l, end - start, ext[1] + tmp_l, (long)occ[0], (long)ovlp.x[2], (long)occ[1]);
for (i = 0; i < cmp[0].l; ++i)
kputc("$ACGTN"[(int)cmp[0].s[i]], s);
kputc('\t', s);
if (qual) kputsn(&qual[pos], cmp[0].l, s);
else kputc('*', s);
} else {
ksprintf(s, "-\t%d\t%d\t%d\t%ld\t%ld\t%ld\t", ext[1] + tmp_l, end - start, ext[0] + tmp_l, (long)occ[1], (long)ovlp.x[2], (long)occ[0]);
for (i = 0; i < cmp[0].l; ++i)
kputc("$ACGTN"[(int)cmp[1].s[i]], s);
kputc('\t', s);
if (qual) {
for (i = pos + cmp[0].l - 1; i >= pos; --i)
kputc(qual[i], s);
} else kputc('*', s);
}
kputc('\n', s);
}
static void worker(void *data, long jid, int tid)
{
global_t *g = (global_t*)data;
thrmem_t *m = &g->mem[tid];
char *seq = g->seq[jid], *qual = g->qual? g->qual[jid] : 0;
int l_seq;
l_seq = strlen(seq);
seq_char2nt6(l_seq, (uint8_t*)seq);
m->str.l = 0;
ksprintf(&m->str, "SQ\t%s\t%d\n", g->name[jid], l_seq);
if (!g->partial) { // full-length match
int64_t k, l, u;
fm_exact(g->e, seq, &l, &u);
if (l < u) {
ksprintf(&m->str, "EM\t0\t%d\t%ld", l_seq, (long)(u - l));
if (g->sa && u - l <= g->max_sa_occ) {
for (k = l; k < u; ++k) {
int64_t idx, i;
i = fm_sa(g->e, g->sa, k, &idx);
ksprintf(&m->str, "\t%ld:%ld", (long)idx, (long)i);
}
}
kputc('\n', &m->str);
}
} else { // SMEM
size_t i;
int64_t k;
fmd_smem(g->e, (uint8_t*)seq, &m->smem, g->min_occ, &m->curr, &m->prev);
if (g->discovery) {
int pre;
for (i = 0, pre = -1; i < m->smem.n; ++i) {
fmdsmem_t *p = &m->smem.a[i];
int start = p->ik.info>>32, end = (uint32_t)p->ik.info;
if (end - start < g->kmer) continue; // skip short SMEMs
rld_extend(g->e, &p->ik, p->ok[1], 0);
discover(g->e, pre < 0? 0 : &m->smem.a[pre], p, l_seq, seq, qual, &m->str, m->cmp);
pre = i;
}
discover(g->e, pre < 0? 0 : &m->smem.a[pre], 0, l_seq, seq, qual, &m->str, m->cmp);
} else {
for (i = 0; i < m->smem.n; ++i) {
fmdsmem_t *p = &m->smem.a[i];
uint32_t st = (uint32_t)(p->ik.info>>32), en = (uint32_t)p->ik.info;
if (en - st < g->min_len) continue;
ksprintf(&m->str, "EM\t%u\t%u\t%ld", st, en, (long)p->ik.x[2]);
if (g->sa && p->ik.x[2] < g->max_sa_occ) {
for (k = 0; k < p->ik.x[2]; ++k) {
int64_t idx, j;
j = fm_sa(g->e, g->sa, p->ik.x[0] + k, &idx);
ksprintf(&m->str, "\t%ld:%ld", (long)idx, (long)j);
}
}
kputc('\n', &m->str);
}
}
}
kputsn("//", 2, &m->str);
free(g->qual[jid]); free(g->seq[jid]); free(g->name[jid]);
g->out[jid] = strdup(m->str.s);
}
int main_match(int argc, char *argv[])
{
int i, c, use_mmap = 0, batch_size = 10000000, l_seqs;
gzFile fp;
char *fn_sa = 0;
kseq_t *ks;
global_t g;
memset(&g, 0, sizeof(global_t));
g.max_sa_occ = 10, g.min_occ = 1, g.n_threads = 1, g.kmer = 61, g.min_len = 0;
while ((c = getopt(argc, argv, "Mdps:m:n:b:t:k:l:")) >= 0) {
if (c == 'M') use_mmap = 1;
else if (c == 's') fn_sa = optarg;
else if (c == 'l') g.min_len = atoi(optarg);
else if (c == 'm') g.max_sa_occ = atoi(optarg);
else if (c == 'p') g.partial = 1;
else if (c == 'd') g.discovery = g.partial = 1;
else if (c == 'n') g.min_occ = atoi(optarg);
else if (c == 't') g.n_threads = atoi(optarg);
else if (c == 'k') g.kmer = atoi(optarg), g.discovery = g.partial = 1;
else if (c == 'b') batch_size = atoi(optarg);
}
if (optind + 2 > argc) {
fprintf(stderr, "Usage: fermi2 match [options] <index.fmd> <seq.fa>\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -p find SMEMs (reqiring both strands in one index)\n");
fprintf(stderr, " -d discovery novel alleles (force -p; experimental)\n");
fprintf(stderr, " -k INT k-mer length in the discovery mode (force -d) [%d]\n", g.kmer);
fprintf(stderr, " -t INT number of threads [%d]\n", g.n_threads);
fprintf(stderr, " -b INT batch size [%d]\n", batch_size);
fprintf(stderr, " -s FILE sampled suffix array []\n");
fprintf(stderr, " -m INT show coordinate if the number of hits is no more than INT [%d]\n", g.max_sa_occ);
fprintf(stderr, " -n INT min occurrences [%d]\n", g.min_occ);
fprintf(stderr, " -l INT min length [%d]\n", g.min_len);
fprintf(stderr, "Output format:\n");
fprintf(stderr, " SQ seqName seqLen\n");
fprintf(stderr, " EM start end occurrence [positions]\n");
// fprintf(stderr, " NS start leftLen diffLen rightLen leftOcc rightOcc strand seq qual\n");
// fprintf(stderr, " At an 'NS' line, the length of 'seq' always equals leftLen+diffLen+rightLen.\n");
return 1;
}
fp = gzopen(argv[optind+1], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the sequence file\n", __func__);
return 1;
}
g.e = use_mmap? rld_restore_mmap(argv[optind]) : rld_restore(argv[optind]);
if (g.e == 0) {
fprintf(stderr, "[E::%s] failed to open the index file\n", __func__);
gzclose(fp);
return 1;
}
if (g.partial && (g.e->mcnt[2] != g.e->mcnt[5] || g.e->mcnt[3] != g.e->mcnt[4])) {
fprintf(stderr, "[E::%s] with '-p', the index must include both strands\n", __func__);
rld_destroy((rld_t*)g.e);
gzclose(fp);
return 1;
}
if (fn_sa) g.sa = fm_sa_restore(fn_sa);
if (fn_sa && g.sa == 0) {
fprintf(stderr, "[E::%s] failed to open the sampled SA file\n", __func__);
rld_destroy((rld_t*)g.e);
gzclose(fp);
return 1;
}
g.mem = calloc(g.n_threads, sizeof(thrmem_t));
batch_size *= g.n_threads;
ks = kseq_init(fp);
l_seqs = 0;
while (kseq_read(ks) >= 0) {
if (g.n_seqs == g.m_seqs) {
g.m_seqs = g.m_seqs? g.m_seqs<<1 : 4;
g.name = realloc(g.name, g.m_seqs * sizeof(char*));
g.seq = realloc(g.seq, g.m_seqs * sizeof(char*));
g.qual = realloc(g.qual, g.m_seqs * sizeof(char*));
g.out = realloc(g.out, g.m_seqs * sizeof(char*));
}
g.name[g.n_seqs] = strdup(ks->name.s);
g.seq[g.n_seqs] = strdup(ks->seq.s);
g.qual[g.n_seqs] = ks->qual.l? strdup(ks->qual.s) : 0; // these will be free'd in worker
++g.n_seqs;
l_seqs += ks->seq.l;
if (l_seqs >= batch_size) {
kt_for(g.n_threads, worker, &g, g.n_seqs);
for (i = 0; i < g.n_seqs; ++i) {
puts(g.out[i]);
free(g.out[i]);
}
g.n_seqs = l_seqs = 0;
}
}
// the last batch
kt_for(g.n_threads, worker, &g, g.n_seqs);
for (i = 0; i < g.n_seqs; ++i) {
puts(g.out[i]);
free(g.out[i]);
}
kseq_destroy(ks);
for (i = 0; i < g.n_threads; ++i) {
free(g.mem[i].curr.a); free(g.mem[i].prev.a); free(g.mem[i].smem.a);
free(g.mem[i].cmp[0].s); free(g.mem[i].cmp[1].s); free(g.mem[i].str.s);
}
free(g.name); free(g.seq); free(g.qual); free(g.out); free(g.mem);
if (g.sa) fm_sa_destroy((fmsa_t*)g.sa);
rld_destroy((rld_t*)g.e);
gzclose(fp);
return 0;
}