r807: allow to change block size in bwt_gen

For a very large reference genome, the default is too small.

bwt.h

@@ -92,6 +92,7 @@ extern "C" {
 	void bwt_destroy(bwt_t *bwt);
 
 	void bwt_bwtgen(const char *fn_pac, const char *fn_bwt); // from BWT-SW
+	void bwt_bwtgen2(const char *fn_pac, const char *fn_bwt, int block_size); // from BWT-SW
 	void bwt_cal_sa(bwt_t *bwt, int intv);
 
 	void bwt_bwtupdate_core(bwt_t *bwt);

bwt_gen.c

@@ -1598,15 +1598,20 @@ void BWTSaveBwtCodeAndOcc(const BWT *bwt, const char *bwtFileName, const char *o
 	}
 }
 
-void bwt_bwtgen(const char *fn_pac, const char *fn_bwt)
+void bwt_bwtgen2(const char *fn_pac, const char *fn_bwt, int block_size)
 {
 	BWTInc *bwtInc;
-	bwtInc = BWTIncConstructFromPacked(fn_pac, 10000000, 10000000);
+	bwtInc = BWTIncConstructFromPacked(fn_pac, block_size, block_size);
 	printf("[bwt_gen] Finished constructing BWT in %u iterations.\n", bwtInc->numberOfIterationDone);
 	BWTSaveBwtCodeAndOcc(bwtInc->bwt, fn_bwt, 0);
 	BWTIncFree(bwtInc);
 }
 
+void bwt_bwtgen(const char *fn_pac, const char *fn_bwt)
+{
+	bwt_bwtgen2(fn_pac, fn_bwt, 10000000);
+}
+
 int bwt_bwtgen_main(int argc, char *argv[])
 {
 	if (argc < 3) {

bwtindex.c

@@ -189,11 +189,11 @@ 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;
+	int c, algo_type = 0, is_64 = 0, block_size = 10000000;
 	clock_t t;
 	int64_t l_pac;
 
-	while ((c = getopt(argc, argv, "6a:p:")) >= 0) {
+	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, "div") == 0) algo_type = 1;
@@ -203,20 +203,25 @@ int bwa_index(int argc, char *argv[]) // the "index" command
 			break;
 		case 'p': prefix = strdup(optarg); break;
 		case '6': is_64 = 1; break;
+		case 'b':
+			block_size = strtol(optarg, &str, 10);
+			if (*str == 'G' || *str == 'g') block_size *= 1024 * 1024 * 1024;
+			else if (*str == 'M' || *str == 'm') block_size *= 1024 * 1024;
+			else if (*str == 'K' || *str == 'k') block_size *= 1024;
 		default: return 1;
 		}
 	}
 
 	if (optind + 1 > argc) {
 		fprintf(stderr, "\n");
-		fprintf(stderr, "Usage:   bwa index [-a bwtsw|is] [-c] <in.fasta>\n\n");
+		fprintf(stderr, "Usage:   bwa index [options] <in.fasta>\n\n");
 		fprintf(stderr, "Options: -a STR    BWT construction algorithm: bwtsw or is [auto]\n");
 		fprintf(stderr, "         -p STR    prefix of the index [same as fasta name]\n");
+		fprintf(stderr, "         -b INT    block size for the bwtsw algorithm (force -a bwtsw) [%d]\n", block_size);
 		fprintf(stderr, "         -6        index files named as <in.fasta>.64.* instead of <in.fasta>.* \n");
 		fprintf(stderr, "\n");
 		fprintf(stderr,	"Warning: `-a bwtsw' does not work for short genomes, while `-a is' and\n");
-		fprintf(stderr, "         `-a div' do not work not for long genomes. Please choose `-a'\n");
+		fprintf(stderr, "         `-a div' do not work not for long genomes.\n\n");
-		fprintf(stderr, "         according to the length of the genome.\n\n");
 		return 1;
 	}
 	if (prefix == 0) {
@@ -242,7 +247,7 @@ int bwa_index(int argc, char *argv[]) // the "index" command
 		strcpy(str2, prefix); strcat(str2, ".bwt");
 		t = clock();
 		fprintf(stderr, "[bwa_index] Construct BWT for the packed sequence...\n");
-		if (algo_type == 2) bwt_bwtgen(str, str2);
+		if (algo_type == 2) bwt_bwtgen2(str, str2, block_size);
 		else if (algo_type == 1 || algo_type == 3) {
 			bwt_t *bwt;
 			bwt = bwt_pac2bwt(str, algo_type == 3);

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r789"
+#define PACKAGE_VERSION "0.7.10-r807-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);