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cleanup index loading code

This commit is contained in:
Heng Li 2013-02-23 16:10:48 -05:00
parent 67543f19a1
commit cfa7165036
6 changed files with 72 additions and 61 deletions
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67
bwa.c
View File

@ -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)
{
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;
}
}
}
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
bwt = bwt_restore_bwt(tmp);
strcat(strcpy(tmp, prefix), ".sa"); // partial suffix array (SA)
bwt_restore_sa(tmp, bwt);
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) {
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_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;
}
fclose(idx->bns->fp_pac);
idx->bns->fp_pac = 0;
}
free(prefix);
return idx;
}

6
bwa.h
View File

@ -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

4
bwape.c
View File

@ -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;

4
bwase.c
View File

@ -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;

29
bwtaln.c
View File

@ -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;

23
bwtsw2_main.c
View File

@ -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;
char buf[1024], *prefix;
bntseq_t *bns;
bwaidx_t *idx;
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) {
fprintf(stderr, "[%s] fail to locate the index\n", __func__);
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);
bns_destroy(bns);
bwt_destroy(target);
free(opt); free(prefix);
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 0;
bsw2_aln(opt, idx->bns, idx->bwt, argv[optind+1], optind+2 < argc? argv[optind+2] : 0);
bwa_idx_destroy(idx);
free(opt);
return 0;
}