preliminary code to generate fake sam

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);
+		if (mem_only) printf("SQ\t%s\t%ld\n", seq->name.s, seq->seq.l);
-		for (i = 0; i < mem.n; ++i) {
+		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;
+					fmhit_t z;
-					int64_t pos;
+					z.tbeg = bwt_sa(bwt, p->x[0] + k);
-					pos = bns_depos(bns, bwt_sa(bwt, p->x[0] + k), &is_rev);
+					z.qbeg = p->info>>32;
-					printf("\t%c%ld", is_rev?'-':'+', (long)pos);
+					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);