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r750: check puts() return (#132 & #103)

This commit is contained in:
Heng Li 2018-03-22 11:31:58 -04:00
parent 18659118cd
commit 623b5d9d48
5 changed files with 24 additions and 7 deletions
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5
format.c
View File

@ -118,7 +118,7 @@ void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int
if (idx) {
uint32_t i;
for (i = 0; i < idx->n_seq; ++i)
printf("@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
mm_sprintf_lite(&str, "@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
}
if (rg) sam_write_rg_line(&str, rg);
mm_sprintf_lite(&str, "@PG\tID:minimap2\tPN:minimap2");
@ -129,8 +129,7 @@ void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int
for (i = 1; i < argc; ++i)
mm_sprintf_lite(&str, " %s", argv[i]);
}
mm_sprintf_lite(&str, "\n");
fputs(str.s, stdout);
mm_err_puts(str.s);
free(str.s);
}

7
main.c
View File

@ -10,7 +10,7 @@
#include "getopt.h"
#endif
#define MM_VERSION "2.9-r749-dirty"
#define MM_VERSION "2.9-r750-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -336,6 +336,11 @@ int main(int argc, char *argv[])
}
mm_idx_reader_close(idx_rdr);
if (fflush(stdout) == EOF) {
fprintf(stderr, "[ERROR] failed to write the results\n");
exit(EXIT_FAILURE);
}
if (mm_verbose >= 3) {
fprintf(stderr, "[M::%s] Version: %s\n", __func__, MM_VERSION);
fprintf(stderr, "[M::%s] CMD:", __func__);

6
map.c
View File

@ -489,11 +489,11 @@ static void *worker_pipeline(void *shared, int step, void *in)
mm_write_sam2(&p->str, mi, t, i - seg_st, j, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
else
mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
puts(p->str.s);
mm_err_puts(p->str.s);
}
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) { // write an unmapped record
mm_write_sam2(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
puts(p->str.s);
mm_err_puts(p->str.s);
}
}
for (i = seg_st; i < seg_en; ++i) {

11
misc.c
View File

@ -1,3 +1,4 @@
#include <stdlib.h>
#include "mmpriv.h"
int mm_verbose = 1;
@ -120,6 +121,16 @@ double realtime(void)
return tp.tv_sec + tp.tv_usec * 1e-6;
}
void mm_err_puts(const char *str)
{
int ret;
ret = puts(str);
if (ret == EOF) {
fprintf(stderr, "[ERROR] failed to write the results\n");
exit(EXIT_FAILURE);
}
}
#include "ksort.h"
#define sort_key_128x(a) ((a).x)

2
mmpriv.h
View File

@ -86,6 +86,8 @@ mm_seg_t *mm_seg_gen(void *km, uint32_t hash, int n_segs, const int *qlens, int
void mm_seg_free(void *km, int n_segs, mm_seg_t *segs);
void mm_pair(void *km, int max_gap_ref, int dp_bonus, int sub_diff, int match_sc, const int *qlens, int *n_regs, mm_reg1_t **regs);
void mm_err_puts(const char *str);
#ifdef __cplusplus
}
#endif