diff --git a/fastmap.c b/fastmap.c index e3485fc..c0c040a 100644 --- a/fastmap.c +++ b/fastmap.c @@ -8,22 +8,121 @@ #include "kseq.h" KSEQ_INIT(gzFile, gzread) +typedef struct { + int qbeg, len; + int64_t tbeg; +} fmhit_t; + +#define hit_qlt(a, b) ((a).qbeg < (b).qbeg) +#define hit_tlt(a, b) ((a).tbeg < (b).tbeg) + +#include "ksort.h" +KSORT_INIT(hitq, fmhit_t, hit_qlt) +KSORT_INIT(hitt, fmhit_t, hit_tlt) + extern unsigned char nst_nt4_table[256]; +typedef struct { size_t n, m; fmhit_t *a; } fmhit_v; + +static uint64_t cluster_qhits(fmhit_v *hits, int beg, int end, int max_dist, int *_score) +{ + int qend, score, max = 0, cbeg = beg; + size_t i; + uint64_t max_cluster = 0; + ks_introsort(hitq, end - beg, hits->a + beg); + qend = hits->a[beg].qbeg + hits->a[beg].len; + score = hits->a[beg].len; + for (i = beg + 1; i < end; ++i) { + fmhit_t *p = &hits->a[i]; + if (p->qbeg - qend > max_dist) { + if (score > max) max = score, max_cluster = (uint64_t)cbeg<<32 | i; + score = 0; cbeg = i; + } + score += p->len; + qend = p->qbeg + p->len; + } + if (score > max) max = score, max_cluster = (uint64_t)cbeg<<32 | i; + *_score = score; + return max_cluster; +} + +static int cluster_hits(fmhit_v *hits, int max_dist) +{ + size_t i; + int64_t tend; + uint64_t cluster, max_cluster = 0; + int j, score, max = 0, max2 = 0, cbeg = 0, cend; + ks_introsort(hitt, hits->n, hits->a); + tend = hits->a[0].tbeg + hits->a[0].len; + for (i = 1; i < hits->n; ++i) { + fmhit_t *p = &hits->a[i]; + if (p->tbeg - tend > max_dist) { + cluster = cluster_qhits(hits, cbeg, i, max_dist, &score); + if (score > max) max2 = max, max = score, max_cluster = cluster; + else if (score > max2) max2 = score; + cbeg = i; + } + tend = p->tbeg + p->len; + } + cluster = cluster_qhits(hits, cbeg, i, max_dist, &score); + if (score > max) max2 = max, max = score, max_cluster = cluster; + else if (score > max2) max2 = score; + cbeg = max_cluster>>32; cend = (uint32_t)max_cluster; + for (i = 0, j = cbeg; j < cend; ++j) hits->a[i++] = hits->a[j]; + hits->n = i; + return (int)(200.0 * (max - max2) / max + .499); +} + +static int fake_cigar(const bntseq_t *bns, fmhit_v *hits, int beg, int end, int len, uint32_t *cigar, int64_t *pos, int *is_rev) +{ + size_t i; + int qbeg, qend, n_cigar = 0; + int64_t tbeg, tend, tmp; + qbeg = len; qend = 0; + tbeg = bns->l_pac<<1; tend = 0; + for (i = beg; i < end; ++i) { + fmhit_t *p = &hits->a[i]; + if (p->qbeg < qbeg) qbeg = p->qbeg; + if (p->qbeg + p->len > qend) qend = p->qbeg + p->len; + if (p->tbeg < tbeg) tbeg = p->tbeg; + if (p->tbeg + p->len > qend) tend = p->tbeg + p->len; + } + if (tbeg >= bns->l_pac) { + tmp = tend; tend = bns->l_pac*2 - tbeg; tbeg = bns->l_pac*2 - tmp; + tmp = qend; qend = len - qbeg; qbeg = len - tmp; + *is_rev = 1; + } else *is_rev = 0; + *pos = tbeg; + if (qbeg) cigar[n_cigar++] = qbeg<<4|4; + if (tend - tbeg < qend - qbeg) { // reference is shorter + cigar[n_cigar++] = (uint32_t)(tend - tbeg)<<4 | 0; + cigar[n_cigar++] = (uint32_t)((qend - qbeg) - (tend - tbeg))<<4 | 2; + } else if (tend - tbeg > qend - qbeg) { // query is shorter + cigar[n_cigar++] = (uint32_t)(qend - qbeg)<<4 | 0; + cigar[n_cigar++] = (uint32_t)((tend - tbeg) - (qend - qbeg))<<4 | 1; + } else cigar[n_cigar++] = (uint32_t)(qend - qbeg)<<4 | 0; + if (len > qend) cigar[n_cigar++] = (uint32_t)(len - qend)<<4|4; + return n_cigar; +} + int main_fastmap(int argc, char *argv[]) { - int c, i, min_iwidth = 3, min_len = 17; + int c, i, min_iwidth = 3, min_len = 17, max_dist = 100, mem_only = 0; kseq_t *seq; bwtint_t k; gzFile fp; bwt_t *bwt; bntseq_t *bns; bwtintv_v a[3], mem, *tvec[3]; + fmhit_v hits; + uint32_t cigar[1024]; - while ((c = getopt(argc, argv, "w:l:")) >= 0) { + while ((c = getopt(argc, argv, "w:l:d:p")) >= 0) { switch (c) { case 'w': min_iwidth = atoi(optarg); break; case 'l': min_len = atoi(optarg); break; + case 'd': max_dist = atoi(optarg); break; + case 'p': mem_only = 1; break; } } if (optind + 1 >= argc) { @@ -46,27 +145,45 @@ int main_fastmap(int argc, char *argv[]) kv_init(a[i]); tvec[i] = &a[i]; } - kv_init(mem); + kv_init(mem); kv_init(hits); while (kseq_read(seq) >= 0) { for (i = 0; i < seq->seq.l; ++i) seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]]; bwt_smem(bwt, seq->seq.l, (uint8_t*)seq->seq.s, &mem, tvec); - printf(">%s\t%ld\n", seq->name.s, seq->seq.l); - for (i = 0; i < mem.n; ++i) { + if (mem_only) printf("SQ\t%s\t%ld\n", seq->name.s, seq->seq.l); + for (i = 0, hits.n = 0; i < mem.n; ++i) { bwtintv_t *p = &mem.a[i]; if ((uint32_t)p->info - (p->info>>32) < min_len) continue; - printf("%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]); + if (mem_only) printf("EM\t%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]); if (p->x[2] <= min_iwidth) { for (k = 0; k < p->x[2]; ++k) { - int is_rev; - int64_t pos; - pos = bns_depos(bns, bwt_sa(bwt, p->x[0] + k), &is_rev); - printf("\t%c%ld", is_rev?'-':'+', (long)pos); + fmhit_t z; + z.tbeg = bwt_sa(bwt, p->x[0] + k); + z.qbeg = p->info>>32; + z.len = (uint32_t)p->info - z.qbeg; + kv_push(fmhit_t, hits, z); + if (mem_only) { + int is_rev, ref_id; + int64_t pos = bns_depos(bns, z.tbeg, &is_rev); + if (is_rev) pos -= z.len - 1; + bns_cnt_ambi(bns, pos, z.len, &ref_id); + printf("\t%s:%c%ld", bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - bns->anns[ref_id].offset) + 1); + } } } - putchar('\n'); + if (mem_only) putchar('\n'); } - puts("//"); + if (!mem_only) { + int64_t pos; + int n_cigar, is_rev, ref_id, mapq; + mapq = cluster_hits(&hits, max_dist); + n_cigar = fake_cigar(bns, &hits, 0, hits.n, seq->seq.l, cigar, &pos, &is_rev); + bns_cnt_ambi(bns, pos, 1, &ref_id); + printf("%s\t%d\t%s\t%ld\t%d\t", seq->name.s, is_rev?16:0, bns->anns[ref_id].name, (long)(pos - bns->anns[ref_id].offset) + 1, mapq); + for (i = 0; i < n_cigar; ++i) + printf("%d%c", cigar[i]>>4, "MIDNSHP"[cigar[i]&0xf]); + printf("\t*\t0\t0\t*\t*\n"); + } else puts("//"); } free(mem.a);