cleanup index loading code

bwa.c

@@ -4,6 +4,8 @@
 #include "bwa.h"
 #include "ksw.h"
 
+int bwa_verbose = 3;
+
 /************************
  * Batch FASTA/Q reader *
  ************************/
@@ -98,28 +100,69 @@ ret_gen_cigar:
  * Full index reader *
  *********************/
 
-bwaidx_t *bwa_idx_load(const char *prefix, int which)
+char *bwa_idx_infer_prefix(const char *hint)
 {
-	bwaidx_t *idx;
+	char *prefix;
-	idx = calloc(1, sizeof(bwaidx_t));
+	int l_hint;
-	if (which & BWA_IDX_BWT) {
+	FILE *fp;
-		char *tmp;
+	l_hint = strlen(hint);
+	prefix = malloc(l_hint + 3 + 4 + 1);
+	strcpy(prefix, hint);
+	strcpy(prefix + l_hint, ".64.bwt");
+	if ((fp = fopen(prefix, "rb")) != 0) {
+		fclose(fp);
+		prefix[l_hint + 3] = 0;
+		return prefix;
+	} else {
+		strcpy(prefix + l_hint, ".bwt");
+		if ((fp = fopen(prefix, "rb")) == 0) {
+			free(prefix);
+			return 0;
+		} else {
+			fclose(fp);
+			prefix[l_hint] = 0;
+			return prefix;
+		}
+	}
+}
+
+bwt_t *bwa_idx_load_bwt(const char *hint)
+{
+	char *tmp, *prefix;
+	bwt_t *bwt;
+	prefix = bwa_idx_infer_prefix(hint);
+	if (prefix == 0) {
+		if (bwa_verbose >= 1)
+			fprintf(stderr, "[E::%s] fail to locate the index files\n", __func__);
+		return 0;
+	}
 	tmp = calloc(strlen(prefix) + 5, 1);
 	strcat(strcpy(tmp, prefix), ".bwt"); // FM-index
-		idx->bwt = bwt_restore_bwt(tmp);
+	bwt = bwt_restore_bwt(tmp);
 	strcat(strcpy(tmp, prefix), ".sa");  // partial suffix array (SA)
-		bwt_restore_sa(tmp, idx->bwt);
+	bwt_restore_sa(tmp, bwt);
-		free(tmp);
+	free(tmp); free(prefix);
-	}
+	return bwt;
+}
+
+bwaidx_t *bwa_idx_load(const char *hint, int which)
+{
+	bwaidx_t *idx;
+	char *prefix;
+	prefix = bwa_idx_infer_prefix(hint);
+	if (prefix == 0) return 0;
+	idx = calloc(1, sizeof(bwaidx_t));
+	if (which & BWA_IDX_BWT) idx->bwt = bwa_idx_load_bwt(hint);
 	if (which & BWA_IDX_BNS) {
 		idx->bns = bns_restore(prefix);
 		if (which & BWA_IDX_PAC) {
 			idx->pac = calloc(idx->bns->l_pac/4+1, 1);
 			fread(idx->pac, 1, idx->bns->l_pac/4+1, idx->bns->fp_pac); // concatenated 2-bit encoded sequence
-		}
 			fclose(idx->bns->fp_pac);
 			idx->bns->fp_pac = 0;
 		}
+	}
+	free(prefix);
 	return idx;
 }
 

bwa.h

@@ -21,6 +21,8 @@ typedef struct {
 	char *name, *comment, *seq, *qual, *sam;
 } bseq1_t;
 
+extern int bwa_verbose;
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -29,7 +31,9 @@ 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);
 
-	bwaidx_t *bwa_idx_load(const char *prefix, int which);
+	char *bwa_idx_infer_prefix(const char *hint);
+	bwt_t *bwa_idx_load_bwt(const char *hint);
+	bwaidx_t *bwa_idx_load(const char *hint, int which);
 	void bwa_idx_destroy(bwaidx_t *idx);
 
 #ifdef __cplusplus

bwape.c

@@ -10,6 +10,7 @@
 #include "utils.h"
 #include "stdaln.h"
 #include "bwase.h"
+#include "bwa.h"
 
 typedef struct {
 	int n;
@@ -716,7 +717,6 @@ 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;
@@ -762,7 +762,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
 		fprintf(stderr, "\n");
 		return 1;
 	}
-	if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
+	if ((prefix = bwa_idx_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;

bwase.c

@@ -10,6 +10,7 @@
 #include "bntseq.h"
 #include "utils.h"
 #include "kstring.h"
+#include "bwa.h"
 
 int g_log_n[256];
 char *bwa_rg_line, *bwa_rg_id;
@@ -606,7 +607,6 @@ 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) {
@@ -628,7 +628,7 @@ 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;
 	}
-	if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
+	if ((prefix = bwa_idx_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;

bwtaln.c

@@ -11,6 +11,7 @@
 #include "bwtaln.h"
 #include "bwtgap.h"
 #include "utils.h"
+#include "bwa.h"
 
 #ifdef HAVE_PTHREAD
 #include <pthread.h>
@@ -219,32 +220,6 @@ 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, ".64.bwt");
-	if ((fp = fopen(prefix, "rb")) != 0) {
-		fclose(fp);
-		prefix[l_hint + 3] = 0;
-		return prefix;
-	} else {
-		strcpy(prefix + l_hint, ".bwt");
-		if ((fp = fopen(prefix, "rb")) == 0) {
-			free(prefix);
-			return 0;
-		} else {
-			fclose(fp);
-			prefix[l_hint] = 0;
-			return prefix;
-		}
-	}
-}
-
 int bwa_aln(int argc, char *argv[])
 {
 	int c, opte = -1;
@@ -328,7 +303,7 @@ int bwa_aln(int argc, char *argv[])
 			k = l;
 		}
 	}
-	if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
+	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
 		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
 		free(opt);
 		return 0;

bwtsw2_main.c

@@ -6,14 +6,12 @@
 #include "bwt.h"
 #include "bwtsw2.h"
 #include "utils.h"
+#include "bwa.h"
 
 int bwa_bwtsw2(int argc, char *argv[])
 {
-	extern char *bwa_infer_prefix(const char *hint);
 	bsw2opt_t *opt;
-	bwt_t *target;
+	bwaidx_t *idx;
-	char buf[1024], *prefix;
-	bntseq_t *bns;
 	int c;
 
 	opt = bsw2_init_opt();
@@ -81,19 +79,10 @@ int bwa_bwtsw2(int argc, char *argv[])
 	opt->t *= opt->a;
 	opt->coef *= opt->a;
 
-	if ((prefix = bwa_infer_prefix(argv[optind])) == 0) {
+	if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 0;
-		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
+	bsw2_aln(opt, idx->bns, idx->bwt, argv[optind+1], optind+2 < argc? argv[optind+2] : 0);
-		return 0;
+	bwa_idx_destroy(idx);
-	}
+	free(opt);
-	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);
-
-	bns_destroy(bns);
-	bwt_destroy(target);
-	free(opt); free(prefix);
 	
 	return 0;
 }