diff --git a/Makefile b/Makefile
index 726cdf2..7151435 100644
--- a/Makefile
+++ b/Makefile
@@ -4,9 +4,10 @@ CFLAGS=		-g -Wall -Wno-unused-function -O2
 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
 AR=			ar
 DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
-LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
-AOBJS=		QSufSort.o bwt_gen.o rope.o rle.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
-			is.o bwtindex.o bwape.o kopen.o pemerge.o maxk.o \
+LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \
+			QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
+AOBJS=		bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
+			bwape.o kopen.o pemerge.o maxk.o \
 			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
 			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
 PROG=		bwa
@@ -63,7 +64,7 @@ bwt_gen.o: QSufSort.h malloc_wrap.h
 bwt_lite.o: bwt_lite.h malloc_wrap.h
 bwtaln.o: bwtaln.h bwt.h bwtgap.h utils.h bwa.h bntseq.h malloc_wrap.h
 bwtgap.o: bwtgap.h bwt.h bwtaln.h malloc_wrap.h
-bwtindex.o: bntseq.h bwt.h utils.h rle.h rope.h malloc_wrap.h
+bwtindex.o: bntseq.h bwa.h bwt.h utils.h rle.h rope.h malloc_wrap.h
 bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h kstring.h
 bwtsw2_aux.o: malloc_wrap.h bwa.h ksw.h kseq.h ksort.h
 bwtsw2_chain.o: bwtsw2.h bntseq.h bwt_lite.h bwt.h malloc_wrap.h ksort.h
diff --git a/bwa.h b/bwa.h
index 1541c1c..aa21725 100644
--- a/bwa.h
+++ b/bwa.h
@@ -12,6 +12,11 @@
 
 #define BWA_CTL_SIZE 0x10000
 
+#define BWTALGO_AUTO  0
+#define BWTALGO_RB2   1
+#define BWTALGO_BWTSW 2
+#define BWTALGO_IS    3
+
 typedef struct {
 	bwt_t    *bwt; // FM-index
 	bntseq_t *bns; // information on the reference sequences
@@ -41,6 +46,8 @@ extern "C" {
 	uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
 	uint32_t *bwa_gen_cigar2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
 
+	int bwa_idx_build(const char *fa, const char *prefix, int algo_type, int block_size);
+
 	char *bwa_idx_infer_prefix(const char *hint);
 	bwt_t *bwa_idx_load_bwt(const char *hint);
 
diff --git a/bwtindex.c b/bwtindex.c
index 826bb5a..fb32231 100644
--- a/bwtindex.c
+++ b/bwtindex.c
@@ -32,6 +32,7 @@
 #include <time.h>
 #include <zlib.h>
 #include "bntseq.h"
+#include "bwa.h"
 #include "bwt.h"
 #include "utils.h"
 #include "rle.h"
@@ -208,19 +209,14 @@ int bwa_bwt2sa(int argc, char *argv[]) // the "bwt2sa" command
 
 int bwa_index(int argc, char *argv[]) // the "index" command
 {
-	extern void bwa_pac_rev_core(const char *fn, const char *fn_rev);
-
-	char *prefix = 0, *str, *str2, *str3;
-	int c, algo_type = 0, is_64 = 0, block_size = 10000000;
-	clock_t t;
-	int64_t l_pac;
-
+	int c, algo_type = BWTALGO_AUTO, is_64 = 0, block_size = 10000000;
+	char *prefix = 0, *str;
 	while ((c = getopt(argc, argv, "6a:p:b:")) >= 0) {
 		switch (c) {
 		case 'a': // if -a is not set, algo_type will be determined later
-			if (strcmp(optarg, "rb2") == 0) algo_type = 1;
-			else if (strcmp(optarg, "bwtsw") == 0) algo_type = 2;
-			else if (strcmp(optarg, "is") == 0) algo_type = 3;
+			if (strcmp(optarg, "rb2") == 0) algo_type = BWTALGO_RB2;
+			else if (strcmp(optarg, "bwtsw") == 0) algo_type = BWTALGO_BWTSW;
+			else if (strcmp(optarg, "is") == 0) algo_type = BWTALGO_IS;
 			else err_fatal(__func__, "unknown algorithm: '%s'.", optarg);
 			break;
 		case 'p': prefix = strdup(optarg); break;
@@ -252,16 +248,29 @@ int bwa_index(int argc, char *argv[]) // the "index" command
 		strcpy(prefix, argv[optind]);
 		if (is_64) strcat(prefix, ".64");
 	}
+	bwa_idx_build(argv[optind], prefix, algo_type, block_size);
+	free(prefix);
+	return 0;
+}
+
+int bwa_idx_build(const char *fa, const char *prefix, int algo_type, int block_size)
+{
+	extern void bwa_pac_rev_core(const char *fn, const char *fn_rev);
+
+	char *str, *str2, *str3;
+	clock_t t;
+	int64_t l_pac;
+
 	str  = (char*)calloc(strlen(prefix) + 10, 1);
 	str2 = (char*)calloc(strlen(prefix) + 10, 1);
 	str3 = (char*)calloc(strlen(prefix) + 10, 1);
 
 	{ // nucleotide indexing
-		gzFile fp = xzopen(argv[optind], "r");
+		gzFile fp = xzopen(fa, "r");
 		t = clock();
-		fprintf(stderr, "[bwa_index] Pack FASTA... ");
+		if (bwa_verbose >= 3) fprintf(stderr, "[bwa_index] Pack FASTA... ");
 		l_pac = bns_fasta2bntseq(fp, prefix, 0);
-		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+		if (bwa_verbose >= 3) fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
 		err_gzclose(fp);
 	}
 	if (algo_type == 0) algo_type = l_pac > 50000000? 2 : 3; // set the algorithm for generating BWT
@@ -269,7 +278,7 @@ int bwa_index(int argc, char *argv[]) // the "index" command
 		strcpy(str, prefix); strcat(str, ".pac");
 		strcpy(str2, prefix); strcat(str2, ".bwt");
 		t = clock();
-		fprintf(stderr, "[bwa_index] Construct BWT for the packed sequence...\n");
+		if (bwa_verbose >= 3) fprintf(stderr, "[bwa_index] Construct BWT for the packed sequence...\n");
 		if (algo_type == 2) bwt_bwtgen2(str, str2, block_size);
 		else if (algo_type == 1 || algo_type == 3) {
 			bwt_t *bwt;
@@ -277,25 +286,25 @@ int bwa_index(int argc, char *argv[]) // the "index" command
 			bwt_dump_bwt(str2, bwt);
 			bwt_destroy(bwt);
 		}
-		fprintf(stderr, "[bwa_index] %.2f seconds elapse.\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+		if (bwa_verbose >= 3) fprintf(stderr, "[bwa_index] %.2f seconds elapse.\n", (float)(clock() - t) / CLOCKS_PER_SEC);
 	}
 	{
 		bwt_t *bwt;
 		strcpy(str, prefix); strcat(str, ".bwt");
 		t = clock();
-		fprintf(stderr, "[bwa_index] Update BWT... ");
+		if (bwa_verbose >= 3) fprintf(stderr, "[bwa_index] Update BWT... ");
 		bwt = bwt_restore_bwt(str);
 		bwt_bwtupdate_core(bwt);
 		bwt_dump_bwt(str, bwt);
 		bwt_destroy(bwt);
-		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+		if (bwa_verbose >= 3) fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
 	}
 	{
-		gzFile fp = xzopen(argv[optind], "r");
+		gzFile fp = xzopen(fa, "r");
 		t = clock();
-		fprintf(stderr, "[bwa_index] Pack forward-only FASTA... ");
+		if (bwa_verbose >= 3) fprintf(stderr, "[bwa_index] Pack forward-only FASTA... ");
 		l_pac = bns_fasta2bntseq(fp, prefix, 1);
-		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+		if (bwa_verbose >= 3) fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
 		err_gzclose(fp);
 	}
 	{
@@ -303,13 +312,13 @@ int bwa_index(int argc, char *argv[]) // the "index" command
 		strcpy(str, prefix); strcat(str, ".bwt");
 		strcpy(str3, prefix); strcat(str3, ".sa");
 		t = clock();
-		fprintf(stderr, "[bwa_index] Construct SA from BWT and Occ... ");
+		if (bwa_verbose >= 3) fprintf(stderr, "[bwa_index] Construct SA from BWT and Occ... ");
 		bwt = bwt_restore_bwt(str);
 		bwt_cal_sa(bwt, 32);
 		bwt_dump_sa(str3, bwt);
 		bwt_destroy(bwt);
-		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+		if (bwa_verbose >= 3) fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
 	}
-	free(str3); free(str2); free(str); free(prefix);
+	free(str3); free(str2); free(str);
 	return 0;
 }