r308: added a new API to convert region to CIGAR

and an example program demonstrating how to do single-end alignment in <50
lines of C code.

Makefile

@@ -8,7 +8,7 @@ AOBJS=		QSufSort.o bwt_gen.o stdaln.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamli
 			is.o bwtindex.o bwape.o \
 			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
 			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
-PROG=		bwa
+PROG=		bwa bwamem-lite
 INCLUDES=	
 LIBS=		-lm -lz -lpthread
 SUBDIRS=	.
@@ -25,6 +25,9 @@ all:$(PROG)
 bwa:libbwa.a $(AOBJS) main.o
 		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ $(LIBS) -L. -lbwa
 
+bwamem-lite:libbwa.a example.o
+		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ $(LIBS) -L. -lbwa
+
 libbwa.a:$(LOBJS)
 		$(AR) -csru $@ $(LOBJS)
 

bwamem.c

@@ -679,7 +679,7 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
 	s->sam = str.s;
 }
 
-mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, char *seq)
+mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, char *seq)
 {
 	int i;
 	mem_chain_v chn;
@@ -703,6 +703,32 @@ mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *
 	return regs;
 }
 
+mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, char *seq)
+{ // the difference from mem_align1_core() lies in that this routine calls mem_mark_primary_se()
+	mem_alnreg_v ar;
+	ar = mem_align1_core(opt, bwt, bns, pac, l_seq, seq);
+	mem_mark_primary_se(opt, ar.n, ar.a);
+	return ar;
+}
+
+// This routine is only used for the API purpose
+mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, const mem_alnreg_t *ar)
+{
+	mem_aln_t a;
+	int qb = ar->qb, qe = ar->qe, NM, score, is_rev;
+	int64_t pos, rb = ar->rb, re = ar->re;
+	memset(&a, 0, sizeof(mem_aln_t));
+	a.mapq = mem_approx_mapq_se(opt, ar);
+	bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re);
+	a.cigar = bwa_gen_cigar(opt->mat, opt->q, opt->r, opt->w, bns->l_pac, pac, qe - qb, (uint8_t*)&query[qb], rb, re, &score, &a.n_cigar, &NM);
+	a.NM = NM;
+	pos = bns_depos(bns, rb < bns->l_pac? rb : re - 1, &is_rev);
+	a.is_rev = is_rev;
+	a.rid = bns_pos2rid(bns, pos);
+	a.pos = pos - bns->anns[a.rid].offset;
+	return a;
+}
+
 typedef struct {
 	int start, step, n;
 	const mem_opt_t *opt;
@@ -720,11 +746,11 @@ static void *worker1(void *data)
 	int i;
 	if (!(w->opt->flag&MEM_F_PE)) {
 		for (i = w->start; i < w->n; i += w->step)
-			w->regs[i] = mem_align1(w->opt, w->bwt, w->bns, w->pac, w->seqs[i].l_seq, w->seqs[i].seq);
+			w->regs[i] = mem_align1_core(w->opt, w->bwt, w->bns, w->pac, w->seqs[i].l_seq, w->seqs[i].seq);
 	} else { // for PE we align the two ends in the same thread in case the 2nd read is of worse quality, in which case some threads may be faster/slower
 		for (i = w->start; i < w->n>>1; i += w->step) {
-			w->regs[i<<1|0] = mem_align1(w->opt, w->bwt, w->bns, w->pac, w->seqs[i<<1|0].l_seq, w->seqs[i<<1|0].seq);
-			w->regs[i<<1|1] = mem_align1(w->opt, w->bwt, w->bns, w->pac, w->seqs[i<<1|1].l_seq, w->seqs[i<<1|1].seq);
+			w->regs[i<<1|0] = mem_align1_core(w->opt, w->bwt, w->bns, w->pac, w->seqs[i<<1|0].l_seq, w->seqs[i<<1|0].seq);
+			w->regs[i<<1|1] = mem_align1_core(w->opt, w->bwt, w->bns, w->pac, w->seqs[i<<1|1].l_seq, w->seqs[i<<1|1].seq);
 		}
 	}
 	return 0;

bwamem.h

@@ -49,19 +49,27 @@ typedef struct {
 	int secondary;  // index of the parent hit shadowing the current hit; <0 if primary
 } mem_alnreg_t;
 
+typedef struct { size_t n, m; mem_alnreg_t *a; } mem_alnreg_v;
+
 typedef struct {
 	int low, high, failed;
 	double avg, std;
 } mem_pestat_t;
 
-typedef struct {
+typedef struct { // TODO: This is an intermediate struct only. Better get rid of it.
 	int64_t rb, re;
 	int qb, qe, flag, qual;
 	// optional info
 	int score, sub;
 } bwahit_t;
 
-typedef struct { size_t n, m; mem_alnreg_t *a; } mem_alnreg_v;
+typedef struct { // This struct is only used for the convenience of API.
+	int rid;
+	int pos;
+	uint32_t is_rev:1, mapq:8, NM:23;
+	int n_cigar;
+	uint32_t *cigar;
+} mem_aln_t;
 
 #ifdef __cplusplus
 extern "C" {
@@ -114,6 +122,8 @@ extern "C" {
 	 */
 	mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, char *seq);
 
+	mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, const mem_alnreg_t *ar);
+
 	/**
 	 * Infer the insert size distribution from interleaved alignment regions
 	 *

example.c

@@ -0,0 +1,50 @@
+#include <stdio.h>
+#include <zlib.h>
+#include <string.h>
+#include <assert.h>
+#include "bwamem.h"
+#include "kseq.h" // for the FASTA/Q parser
+KSEQ_DECLARE(gzFile)
+
+int main(int argc, char *argv[])
+{
+	bwaidx_t *idx;
+	gzFile fp;
+	kseq_t *ks;
+	mem_opt_t *opt;
+
+	if (argc < 3) {
+		fprintf(stderr, "Usage: bwamem-lite <idx.base> <reads.fq>\n");
+		return 1;
+	}
+
+	idx = bwa_idx_load(argv[1], BWA_IDX_ALL); // load the BWA index
+	assert(idx);
+	fp = strcmp(argv[2], "-")? gzopen(argv[2], "r") : gzdopen(fileno(stdin), "r");
+	assert(fp);
+	ks = kseq_init(fp); // initialize the FASTA/Q parser
+	opt = mem_opt_init(); // initialize the BWA-MEM parameters to the default values
+
+	while (kseq_read(ks) >= 0) { // read one sequence
+		mem_alnreg_v ar;
+		int i, k;
+		ar = mem_align1(opt, idx->bwt, idx->bns, idx->pac, ks->seq.l, ks->seq.s); // get all the hits
+		for (i = 0; i < ar.n; ++i) { // traverse each hit
+			mem_aln_t a;
+			if (ar.a[i].secondary >= 0) continue; // skip secondary alignments
+			a = mem_reg2aln(opt, idx->bns, idx->pac, (uint8_t*)ks->seq.s, &ar.a[i]); // get forward-strand position and CIGAR
+			printf("%s\t%c\t%s\t%d\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, a.pos, a.mapq);
+			for (k = 0; k < a.n_cigar; ++k)
+				printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]);
+			printf("\t%d\n", a.NM);
+			free(a.cigar); // don't forget to deallocate CIGAR
+		}
+		free(ar.a); // and deallocate the hit list
+	}
+
+	free(opt);
+	kseq_destroy(ks);
+	gzclose(fp);
+	bwa_idx_destroy(idx);
+	return 0;
+}

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.6.2-r306-beta"
+#define PACKAGE_VERSION "0.6.2-r308-beta"
 #endif
 
 static int usage()