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r896: more flexible ALT reading

This commit is contained in:
Heng Li 2014-10-14 23:37:24 -04:00
parent 2a18fa114f
commit 71277f0fea
3 changed files with 19 additions and 6 deletions
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18
bntseq.c
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@ -179,17 +179,25 @@ bntseq_t *bns_restore(const char *prefix)
if ((fp = fopen(strcat(strcpy(alt_filename, prefix), ".alt"), "r")) != 0) { // read .alt file if present if ((fp = fopen(strcat(strcpy(alt_filename, prefix), ".alt"), "r")) != 0) { // read .alt file if present
char str[1024]; char str[1024];
khash_t(str) *h; khash_t(str) *h;
int i, absent; int c, i, absent;
khint_t k; khint_t k;
h = kh_init(str); h = kh_init(str);
for (i = 0; i < bns->n_seqs; ++i) { for (i = 0; i < bns->n_seqs; ++i) {
k = kh_put(str, h, bns->anns[i].name, &absent); k = kh_put(str, h, bns->anns[i].name, &absent);
kh_val(h, k) = i; kh_val(h, k) = i;
} }
while (fscanf(fp, "%s", str) == 1) { i = 0;
k = kh_get(str, h, str); while ((c = fgetc(fp)) != EOF) {
if (k != kh_end(h)) if (c == '\t' || c == '\n' || c == '\r') {
bns->anns[kh_val(h, k)].is_alt = 1; str[i] = 0;
if (str[0] != '@') {
k = kh_get(str, h, str);
if (k != kh_end(h))
bns->anns[kh_val(h, k)].is_alt = 1;
}
while (c != '\n' && c != EOF) c = fgetc(fp);
i = 0;
} else str[i++] = c; // FIXME: potential segfault here
} }
kh_destroy(str, h); kh_destroy(str, h);
fclose(fp); fclose(fp);

5
bwa.c
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@ -239,7 +239,12 @@ bwaidx_t *bwa_idx_load(const char *hint, int which)
idx = calloc(1, sizeof(bwaidx_t)); idx = calloc(1, sizeof(bwaidx_t));
if (which & BWA_IDX_BWT) idx->bwt = bwa_idx_load_bwt(hint); if (which & BWA_IDX_BWT) idx->bwt = bwa_idx_load_bwt(hint);
if (which & BWA_IDX_BNS) { if (which & BWA_IDX_BNS) {
int i, c;
idx->bns = bns_restore(prefix); idx->bns = bns_restore(prefix);
for (i = c = 0; i < idx->bns->n_seqs; ++i)
if (idx->bns->anns[i].is_alt) ++c;
if (bwa_verbose >= 3)
fprintf(stderr, "[M::%s] read %d ALT contigs\n", __func__, c);
if (which & BWA_IDX_PAC) { if (which & BWA_IDX_PAC) {
idx->pac = calloc(idx->bns->l_pac/4+1, 1); idx->pac = calloc(idx->bns->l_pac/4+1, 1);
err_fread_noeof(idx->pac, 1, idx->bns->l_pac/4+1, idx->bns->fp_pac); // concatenated 2-bit encoded sequence err_fread_noeof(idx->pac, 1, idx->bns->l_pac/4+1, idx->bns->fp_pac); // concatenated 2-bit encoded sequence

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r895-dirty" #define PACKAGE_VERSION "0.7.10-r896-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);