migrated minimap/example.c here.

Makefile

@@ -24,6 +24,9 @@ extra:all $(PROG_EXTRA)
 minimap2:main.o libminimap2.a
 		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
 
+minimap2-lite:example.o libminimap2.a
+		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
+
 libminimap2.a:$(OBJS)
 		$(AR) -csru $@ $(OBJS)
 

example.c

@@ -0,0 +1,61 @@
+// To compile:
+//   gcc -g -O2 example.c libminimap2.a -lz
+
+#include <stdlib.h>
+#include <assert.h>
+#include <stdio.h>
+#include <zlib.h>
+#include "minimap.h"
+#include "kseq.h"
+KSEQ_INIT(gzFile, gzread)
+
+int main(int argc, char *argv[])
+{
+	mm_verbose = 2; // disable message output to stderr
+
+	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
+	int n_threads = 4, w = 10, k = 15, is_hpc = 0;
+	mm_idx_t *mi = mm_idx_build(argv[1], w, k, is_hpc, n_threads);
+	assert(mi);
+
+	// mapping
+	mm_mapopt_t opt;
+	mm_mapopt_init(&opt); // initialize mapping parameters
+	mm_mapopt_update(&opt, mi); // this sets the maximum minimizer occurrence; TODO: set a better default in mm_mapopt_init()!
+	opt.flag |= MM_F_CIGAR; // perform alignment
+	mm_tbuf_t *tbuf = mm_tbuf_init(); // thread buffer; for multi-threading, allocate one tbuf for each thread
+	while (kseq_read(ks) >= 0) { // each kseq_read() call reads one query sequence
+		const mm_reg1_t *reg;
+		int j, i, n_reg;
+		// get all hits for the query
+		reg = mm_map(mi, ks->seq.l, ks->seq.s, &n_reg, tbuf, &opt, 0);
+		// traverse hits and print them out
+		for (j = 0; j < n_reg; ++j) {
+			const mm_reg1_t *r = &reg[j];
+			assert(r->p); // with MM_F_CIGAR, this should not be NULL
+			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,
+				   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');
+		}
+	}
+	mm_tbuf_destroy(tbuf);
+
+	// deallocate index and close the query file
+	mm_idx_destroy(mi);
+	kseq_destroy(ks);
+	gzclose(f);
+	return 0;
+}