Tim's suggestion suffix file name with .64

bwape.c

@@ -766,8 +766,11 @@ int bwa_sai2sam_pe(int argc, char *argv[])
 {
 	extern char *bwa_rg_line, *bwa_rg_id;
 	extern int bwa_set_rg(const char *s);
+	extern char *bwa_infer_prefix(const char *hint);
 	int c;
 	pe_opt_t *popt;
+	char *prefix;
+
 	popt = bwa_init_pe_opt();
 	while ((c = getopt(argc, argv, "a:o:sPn:N:c:f:Ar:")) >= 0) {
 		switch (c) {
@@ -809,8 +812,13 @@ int bwa_sai2sam_pe(int argc, char *argv[])
 		fprintf(stderr, "\n");
 		return 1;
 	}
-	bwa_sai2sam_pe_core(argv[optind], argv + optind + 1, argv + optind+3, popt);
+	if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
+		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
 		free(bwa_rg_line); free(bwa_rg_id);
+		return 0;
+	}
+	bwa_sai2sam_pe_core(prefix, argv + optind + 1, argv + optind+3, popt);
+	free(bwa_rg_line); free(bwa_rg_id); free(prefix);
 	free(popt);
 	return 0;
 }

bwase.c

@@ -650,7 +650,9 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
 
 int bwa_sai2sam_se(int argc, char *argv[])
 {
+	extern char *bwa_infer_prefix(const char *hint);
 	int c, n_occ = 3;
+	char *prefix;
 	while ((c = getopt(argc, argv, "hn:f:r:")) >= 0) {
 		switch (c) {
 		case 'h': break;
@@ -670,7 +672,12 @@ int bwa_sai2sam_se(int argc, char *argv[])
 		fprintf(stderr, "Usage: bwa samse [-n max_occ] [-f out.sam] [-r RG_line] <prefix> <in.sai> <in.fq>\n");
 		return 1;
 	}
-	bwa_sai2sam_se_core(argv[optind], argv[optind+1], argv[optind+2], n_occ);
+	if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
+		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
+		free(bwa_rg_line); free(bwa_rg_id);
+		return 0;
+	}
+	bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ);
 	free(bwa_rg_line); free(bwa_rg_id);
 	return 0;
 }

bwtaln.c

@@ -219,10 +219,35 @@ void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
 	bwa_seq_close(ks);
 }
 
+char *bwa_infer_prefix(const char *hint)
+{
+	char *prefix;
+	int l_hint;
+	FILE *fp;
+	l_hint = strlen(hint);
+	prefix = malloc(l_hint + 3 + 4 + 1);
+	strcpy(prefix, hint);
+	strcpy(prefix + l_hint, ".bwt");
+	if ((fp = fopen(prefix, "rb")) != 0) {
+		prefix[l_hint] = 0;
+		return prefix;
+	} else {
+		strcpy(prefix + l_hint, ".64.bwt");
+		if ((fp = fopen(prefix, "rb")) == 0) {
+			free(prefix);
+			return 0;
+		} else {
+			prefix[l_hint + 3] = 0;
+			return prefix;
+		}
+	}
+}
+
 int bwa_aln(int argc, char *argv[])
 {
 	int c, opte = -1;
 	gap_opt_t *opt;
+	char *prefix;
 
 	opt = gap_init_opt();
 	while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:f:b012IYB:")) >= 0) {
@@ -303,10 +328,15 @@ int bwa_aln(int argc, char *argv[])
 			k = l;
 		}
 	}
-	bwa_aln_core(argv[optind], argv[optind+1], opt);
+	if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
+		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
 		free(opt);
 		return 0;
 	}
+	bwa_aln_core(prefix, argv[optind+1], opt);
+	free(opt); free(prefix);
+	return 0;
+}
 
 /* rgoya: Temporary clone of aln_path2cigar to accomodate for bwa_cigar_t,
 __cigar_op and __cigar_len while keeping stdaln stand alone */

bwtindex.c

@@ -72,7 +72,11 @@ int bwa_index(int argc, char *argv[])
 		fprintf(stderr, "         according to the length of the genome.\n\n");
 		return 1;
 	}
-	if (prefix == 0) prefix = strdup(argv[optind]);
+	if (prefix == 0) {
+		prefix = malloc(strlen(argv[optind]) + 4);
+		strcpy(prefix, argv[optind]);
+		strcat(prefix, ".64");
+	}
 	str  = (char*)calloc(strlen(prefix) + 10, 1);
 	str2 = (char*)calloc(strlen(prefix) + 10, 1);
 	str3 = (char*)calloc(strlen(prefix) + 10, 1);

bwtsw2_main.c

@@ -9,9 +9,10 @@
 
 int bwa_bwtsw2(int argc, char *argv[])
 {
+	extern char *bwa_infer_prefix(const char *hint);
 	bsw2opt_t *opt;
 	bwt_t *target;
-	char buf[1024];
+	char buf[1024], *prefix;
 	bntseq_t *bns;
 	int c;
 
@@ -72,9 +73,13 @@ int bwa_bwtsw2(int argc, char *argv[])
 	opt->t *= opt->a;
 	opt->coef *= opt->a;
 
-	strcpy(buf, argv[optind]); target = bwt_restore_bwt(strcat(buf, ".bwt"));
+	if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
-	strcpy(buf, argv[optind]); bwt_restore_sa(strcat(buf, ".sa"), target);
+		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
-	bns = bns_restore(argv[optind]);
+		return 0;
+	}
+	strcpy(buf, prefix); target = bwt_restore_bwt(strcat(buf, ".bwt"));
+	strcpy(buf, prefix); bwt_restore_sa(strcat(buf, ".sa"), target);
+	bns = bns_restore(prefix);
 
 	bsw2_aln(opt, bns, target, argv[optind+1], optind+2 < argc? argv[optind+2] : 0);
 

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.6.1-r104"
+#define PACKAGE_VERSION "0.6.1-r106-master"
 #endif
 
 static int usage()