code refactoring

bwa.c

@@ -94,3 +94,40 @@ ret_gen_cigar:
 	return cigar;
 }
 
+/*********************
+ * Full index reader *
+ *********************/
+
+bwaidx_t *bwa_idx_load(const char *prefix, int which)
+{
+	bwaidx_t *idx;
+	idx = calloc(1, sizeof(bwaidx_t));
+	if (which & BWA_IDX_BWT) {
+		char *tmp;
+		tmp = calloc(strlen(prefix) + 5, 1);
+		strcat(strcpy(tmp, prefix), ".bwt"); // FM-index
+		idx->bwt = bwt_restore_bwt(tmp);
+		strcat(strcpy(tmp, prefix), ".sa");  // partial suffix array (SA)
+		bwt_restore_sa(tmp, idx->bwt);
+		free(tmp);
+	}
+	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;
+	}
+	return idx;
+}
+
+void bwa_idx_destroy(bwaidx_t *idx)
+{
+	if (idx == 0) return;
+	if (idx->bwt) bwt_destroy(idx->bwt);
+	if (idx->bns) bns_destroy(idx->bns);
+	if (idx->pac) free(idx->pac);
+	free(idx);
+}

bwa.h

@@ -2,6 +2,19 @@
 #define BWA_H_
 
 #include <stdint.h>
+#include "bntseq.h"
+#include "bwt.h"
+
+#define BWA_IDX_BWT 0x1
+#define BWA_IDX_BNS 0x2
+#define BWA_IDX_PAC 0x4
+#define BWA_IDX_ALL 0x7
+
+typedef struct {
+	bwt_t    *bwt; // FM-index
+	bntseq_t *bns; // information on the reference sequences
+	uint8_t  *pac; // the actual 2-bit encoded reference sequences with 'N' converted to a random base
+} bwaidx_t;
 
 typedef struct {
 	int l_seq;
@@ -16,6 +29,9 @@ 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);
+	void bwa_idx_destroy(bwaidx_t *idx);
+
 #ifdef __cplusplus
 }
 #endif

bwamem.c

@@ -112,7 +112,6 @@ void smem_set_query(smem_i *itr, int len, const uint8_t *query)
 	itr->len = len;
 }
 
-
 const bwtintv_v *smem_next(smem_i *itr, int split_len, int split_width)
 {
 	int i, max, max_i, ori_start;

fastmap.c

@@ -2,8 +2,7 @@
 #include <stdio.h>
 #include <unistd.h>
 #include <stdlib.h>
-#include "bntseq.h"
+#include "bwa.h"
-#include "bwt.h"
 #include "bwamem.h"
 #include "kvec.h"
 #include "utils.h"
@@ -15,13 +14,11 @@ extern unsigned char nst_nt4_table[256];
 int main_mem(int argc, char *argv[])
 {
 	mem_opt_t *opt;
-	bwt_t *bwt;
-	bntseq_t *bns;
 	int c, n, l;
 	gzFile fp, fp2 = 0;
 	kseq_t *ks, *ks2 = 0;
-	uint8_t *pac = 0;
 	bseq1_t *seqs;
+	bwaidx_t *idx;
 
 	opt = mem_opt_init();
 	while ((c = getopt(argc, argv, "PHk:c:v:s:r:t:")) >= 0) {
@@ -48,19 +45,9 @@ int main_mem(int argc, char *argv[])
 		return 1;
 	}
 	mem_fill_scmat(opt->a, opt->b, opt->mat);
-	{ // load the packed sequences, BWT and SA
+	idx = bwa_idx_load(argv[optind], BWA_IDX_ALL);
-		char *tmp = calloc(strlen(argv[optind]) + 5, 1);
+	for (l = 0; l < idx->bns->n_seqs; ++l)
-		strcat(strcpy(tmp, argv[optind]), ".bwt");
+		printf("@SQ\tSN:%s\tLN:%d\n", idx->bns->anns[l].name, idx->bns->anns[l].len);
-		bwt = bwt_restore_bwt(tmp);
-		strcat(strcpy(tmp, argv[optind]), ".sa");
-		bwt_restore_sa(tmp, bwt);
-		free(tmp);
-		bns = bns_restore(argv[optind]);
-		pac = calloc(bns->l_pac/4+1, 1);
-		fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
-	}
-	for (l = 0; l < bns->n_seqs; ++l)
-		printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[l].name, bns->anns[l].len);
 
 	fp = strcmp(argv[optind + 1], "-")? gzopen(argv[optind + 1], "r") : gzdopen(fileno(stdin), "r");
 	ks = kseq_init(fp);
@@ -70,13 +57,12 @@ int main_mem(int argc, char *argv[])
 		opt->flag |= MEM_F_PE;
 	}
 	while ((seqs = bseq_read(opt->chunk_size, &n, ks, ks2)) != 0) {
-		mem_process_seqs(opt, bwt, bns, pac, n, seqs);
+		mem_process_seqs(opt, idx->bwt, idx->bns, idx->pac, n, seqs);
 		free(seqs);
 	}
 
-	free(opt); free(pac);
+	free(opt);
-	bns_destroy(bns);
+	bwa_idx_destroy(idx);
-	bwt_destroy(bwt);
 	kseq_destroy(ks);
 	gzclose(fp);
 	if (ks2) {
@@ -92,10 +78,9 @@ int main_fastmap(int argc, char *argv[])
 	kseq_t *seq;
 	bwtint_t k;
 	gzFile fp;
-	bwt_t *bwt;
-	bntseq_t *bns;
 	smem_i *itr;
 	const bwtintv_v *a;
+	bwaidx_t *idx;
 
 	while ((c = getopt(argc, argv, "w:l:ps:")) >= 0) {
 		switch (c) {
@@ -112,16 +97,8 @@ int main_fastmap(int argc, char *argv[])
 
 	fp = gzopen(argv[optind + 1], "r");
 	seq = kseq_init(fp);
-	{ // load the packed sequences, BWT and SA
+	idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS);
-		char *tmp = calloc(strlen(argv[optind]) + 5, 1);
+	itr = smem_itr_init(idx->bwt);
-		strcat(strcpy(tmp, argv[optind]), ".bwt");
-		bwt = bwt_restore_bwt(tmp);
-		strcat(strcpy(tmp, argv[optind]), ".sa");
-		bwt_restore_sa(tmp, bwt);
-		free(tmp);
-		bns = bns_restore(argv[optind]);
-	}
-	itr = smem_itr_init(bwt);
 	while (kseq_read(seq) >= 0) {
 		printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);
 		if (print_seq) {
@@ -141,10 +118,10 @@ int main_fastmap(int argc, char *argv[])
 						bwtint_t pos;
 						int len, is_rev, ref_id;
 						len  = (uint32_t)p->info - (p->info>>32);
-						pos = bns_depos(bns, bwt_sa(bwt, p->x[0] + k), &is_rev);
+						pos = bns_depos(idx->bns, bwt_sa(idx->bwt, p->x[0] + k), &is_rev);
 						if (is_rev) pos -= len - 1;
-						bns_cnt_ambi(bns, pos, len, &ref_id);
+						bns_cnt_ambi(idx->bns, pos, len, &ref_id);
-						printf("\t%s:%c%ld", bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - bns->anns[ref_id].offset) + 1);
+						printf("\t%s:%c%ld", idx->bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - idx->bns->anns[ref_id].offset) + 1);
 					}
 				} else fputs("\t*", stdout);
 				putchar('\n');
@@ -154,8 +131,7 @@ int main_fastmap(int argc, char *argv[])
 	}
 
 	smem_itr_destroy(itr);
-	bns_destroy(bns);
+	bwa_idx_destroy(idx);
-	bwt_destroy(bwt);
 	kseq_destroy(seq);
 	gzclose(fp);
 	return 0;