r369: updated example with the latest API

example.c

@@ -11,53 +11,52 @@ KSEQ_INIT(gzFile, gzread)
 
 int main(int argc, char *argv[])
 {
+	mm_idxopt_t iopt;
+	mm_mapopt_t mopt;
+	int n_threads = 3;
+
 	mm_verbose = 2; // disable message output to stderr
+	mm_set_opt(0, &iopt, &mopt);
+	mopt.flag |= MM_F_CIGAR; // perform alignment
 
 	if (argc < 3) {
 		fprintf(stderr, "Usage: minimap2-lite <target.fa> <query.fa>\n");
 		return 1;
 	}
-	
+
 	// open query file for reading; you may use your favorite FASTA/Q parser
 	gzFile f = gzopen(argv[2], "r");
 	assert(f);
 	kseq_t *ks = kseq_init(f);
 
-	// create index for target; we are creating one index for all target sequence
+	// open index reader
-	int n_threads = 4, w = 10, k = 15, is_hpc = 0;
+	mm_idx_reader_t *r = mm_idx_reader_open(argv[1], &iopt, 0);
-	mm_idx_t *mi = mm_idx_build(argv[1], w, k, is_hpc, n_threads);
+	mm_idx_t *mi;
-	assert(mi);
+	while ((mi = mm_idx_reader_read(r, n_threads)) != 0) { // traverse each part of the index
-
+		mm_mapopt_update(&mopt, mi); // this sets the maximum minimizer occurrence; TODO: set a better default in mm_mapopt_init()!
-	// mapping
+		mm_tbuf_t *tbuf = mm_tbuf_init(); // thread buffer; for multi-threading, allocate one tbuf for each thread
-	mm_mapopt_t opt;
+		while (kseq_read(ks) >= 0) { // each kseq_read() call reads one query sequence
-	mm_mapopt_init(&opt); // initialize mapping parameters
+			mm_reg1_t *reg;
-	mm_mapopt_update(&opt, mi); // this sets the maximum minimizer occurrence; TODO: set a better default in mm_mapopt_init()!
+			int j, i, n_reg;
-	opt.flag |= MM_F_CIGAR; // perform alignment
+			reg = mm_map(mi, ks->seq.l, ks->seq.s, &n_reg, tbuf, &mopt, 0); // get all hits for the query
-	mm_tbuf_t *tbuf = mm_tbuf_init(); // thread buffer; for multi-threading, allocate one tbuf for each thread
+			for (j = 0; j < n_reg; ++j) { // traverse hits and print them out
-	while (kseq_read(ks) >= 0) { // each kseq_read() call reads one query sequence
+				mm_reg1_t *r = &reg[j];
-		mm_reg1_t *reg;
+				assert(r->p); // with MM_F_CIGAR, this should not be NULL
-		int j, i, n_reg;
+				printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
-		// get all hits for the query
+				printf("%s\t%d\t%d\t%d\t%d\t%d\t%d\tcg:Z:", mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re,
-		reg = mm_map(mi, ks->seq.l, ks->seq.s, &n_reg, tbuf, &opt, 0);
+						r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen, r->mapq);
-		// traverse hits and print them out
+				for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
-		for (j = 0; j < n_reg; ++j) {
+					printf("%d%c", r->p->cigar[i]>>4, "MIDSHN"[r->p->cigar[i]&0xf]);
-			mm_reg1_t *r = &reg[j];
+				putchar('\n');
-			assert(r->p); // with MM_F_CIGAR, this should not be NULL
+				free(r->p);
-			printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
+			}
-			printf("%s\t%d\t%d\t%d\t%d\t%d\t%d\tcg:Z:", mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re,
+			free(reg);
-				   r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen, r->mapq);
-			for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
-				printf("%d%c", r->p->cigar[i]>>4, "MIDSHN"[r->p->cigar[i]&0xf]);
-			putchar('\n');
-			free(r->p);
 		}
-		free(reg);
+		mm_tbuf_destroy(tbuf);
+		mm_idx_destroy(mi);
 	}
-	mm_tbuf_destroy(tbuf);
+	mm_idx_reader_close(r); // close the index reader
-
+	kseq_destroy(ks); // close the query file
-	// deallocate index and close the query file
-	mm_idx_destroy(mi);
-	kseq_destroy(ks);
 	gzclose(f);
 	return 0;
 }

main.c

@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.1.1-r368-dirty"
+#define MM_VERSION "2.1.1-r369-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -67,6 +67,7 @@ int main(int argc, char *argv[])
 	char *fnw = 0, *rg = 0, *s;
 	FILE *fp_help = stderr;
 	mm_idx_reader_t *idx_rdr;
+	mm_idx_t *mi;
 
 	liftrlimit();
 	mm_realtime0 = realtime();
@@ -210,9 +211,7 @@ int main(int argc, char *argv[])
 	}
 	if (opt.flag & MM_F_OUT_SAM)
 		mm_write_sam_hdr_no_SQ(rg, MM_VERSION, argc, argv);
-	for (;;) {
+	while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0) {
-		mm_idx_t *mi;
-		if ((mi = mm_idx_reader_read(idx_rdr, n_threads)) == 0) break;
 		if (mm_verbose >= 2 && idx_rdr->n_parts > 1 && (opt.flag&MM_F_OUT_SAM) && !(opt.flag&MM_F_NO_SAM_SQ))
 			fprintf(stderr, "[WARNING] \033[1;31mSAM output is malformated due to internal @SQ lines. Please add option --no-sam-sq or filter afterwards.\033[0m\n");
 		if (mm_verbose >= 3)