drop smem based mapping algorithm

While we can compute smems very efficiently, there is still a long way to get
the alignment. On simulated data, this smem-based algorithm is 4X faster than
bwasw and twice as fast as bowtie2, but the accuracy is far lower than bwasw
and even lower than bowtie2 in the high-mapQ range. I am kind of sure that if
we continue to increase the mapping accuracy, the speed will approach to bwasw,
if not slower.

Smem-based mapping algorithm is still interesting, but given that I am short of
time, I will not explore it further.

fastmap.c

@@ -8,125 +8,26 @@
 #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 = 20, min_len = 17, max_dist = 50, mem_only = 0;
+	int c, i, min_iwidth = 20, min_len = 17;
 	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:d:p")) >= 0) {
+	while ((c = getopt(argc, argv, "w:l:")) >= 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) {
-		fprintf(stderr, "bwa fastmap <idxbase> <in.fq>\n");
+		fprintf(stderr, "Usage: bwa fastmap [-l minLen=%d] [-w maxSaSize=%d] <idxbase> <in.fq>\n", min_len, min_iwidth);
 		return 1;
 	}
 
@@ -145,46 +46,30 @@ int main_fastmap(int argc, char *argv[])
 		kv_init(a[i]);
 		tvec[i] = &a[i];
 	}
-	kv_init(mem); kv_init(hits);
+	kv_init(mem);
 	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);
-		if (mem_only) printf("SQ\t%s\t%ld\n", seq->name.s, seq->seq.l);
+		printf("SQ\t%s\t%ld\n", seq->name.s, seq->seq.l);
-		for (i = 0, hits.n = 0; i < mem.n; ++i) {
+		for (i = 0; i < mem.n; ++i) {
 			bwtintv_t *p = &mem.a[i];
 			if ((uint32_t)p->info - (p->info>>32) < min_len) continue;
-			if (mem_only) printf("EM\t%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
+			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) {
-					fmhit_t z;
+					bwtint_t pos;
-					z.tbeg = bwt_sa(bwt, p->x[0] + k);
+					int len, is_rev, ref_id;
-					z.qbeg = p->info>>32;
+					len  = (uint32_t)p->info - (p->info>>32);
-					z.len  = (uint32_t)p->info - z.qbeg;
+					pos = bns_depos(bns, bwt_sa(bwt, p->x[0] + k), &is_rev);
-					kv_push(fmhit_t, hits, z);
+					if (is_rev) pos -= len - 1;
-					if (mem_only) {
+					bns_cnt_ambi(bns, pos, len, &ref_id);
-						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;
-			if (hits.n == 0) continue;
-			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);

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.6.0-r64-dev"
+#define PACKAGE_VERSION "0.6.0-r68-dev"
 #endif
 
 static int usage()
@@ -19,6 +19,7 @@ static int usage()
 	fprintf(stderr, "         samse         generate alignment (single ended)\n");
 	fprintf(stderr, "         sampe         generate alignment (paired ended)\n");
 	fprintf(stderr, "         bwasw         BWA-SW for long queries\n");
+	fprintf(stderr, "         fastmap       identify super-maximal exact matches\n");
 	fprintf(stderr, "\n");
 	fprintf(stderr, "         fa2pac        convert FASTA to PAC format\n");
 	fprintf(stderr, "         pac2bwt       generate BWT from PAC\n");