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Check for whether output is correctly written #132

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Check for whether output is correctly written #132

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6 changes: 4 additions & 2 deletions format.c
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Original file line number Diff line number Diff line change
Expand Up @@ -112,8 +112,9 @@ static void sam_write_rg_line(kstring_t *str, const char *s)
free(rg_line);
}

void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int argc, char *argv[])
int mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int argc, char *argv[])
{
int err;
kstring_t str = {0,0,0};
if (idx) {
uint32_t i;
Expand All @@ -130,8 +131,9 @@ void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int
mm_sprintf_lite(&str, " %s", argv[i]);
}
mm_sprintf_lite(&str, "\n");
fputs(str.s, stdout);
err = fputs(str.s, stdout);
free(str.s);
return err;
}

static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int no_iden)
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15 changes: 13 additions & 2 deletions main.c
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Expand Up @@ -309,13 +309,18 @@ int main(int argc, char *argv[])
return 1;
}
if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) {
int err;
if (mm_idx_reader_eof(idx_rdr)) {
mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
err = mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
} else {
mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
err = mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
if (mm_verbose >= 2)
fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted.\033[0m\n");
}
if (err == EOF) {
fprintf(stderr, "[ERROR] error writing output header\n");
return 1;
}
}
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] loaded/built the index for %d target sequence(s)\n",
Expand All @@ -337,5 +342,11 @@ int main(int argc, char *argv[])
for (i = 0; i < argc; ++i)
fprintf(stderr, " %s", argv[i]);
fprintf(stderr, "\n[M::%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - mm_realtime0, cputime());

int err = fflush(stdout);
if (err == EOF) {
fprintf(stderr, "[ERROR]: Could not flush output\n");
return 1;
}
return 0;
}
7 changes: 5 additions & 2 deletions map.c
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Expand Up @@ -478,6 +478,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
if ((p->opt->flag & MM_F_OUT_CS) && !(mm_dbg_flag & MM_DBG_NO_KALLOC)) km = km_init();
for (k = 0; k < s->n_frag; ++k) {
int seg_st = s->seg_off[k], seg_en = s->seg_off[k] + s->n_seg[k];
int err;
for (i = seg_st; i < seg_en; ++i) {
mm_bseq1_t *t = &s->seq[i];
for (j = 0; j < s->n_reg[i]; ++j) {
Expand All @@ -489,11 +490,13 @@ 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);
err = puts(p->str.s);
if (err == EOF) exit(1);
}
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
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);
err = puts(p->str.s);
if (err == EOF) exit(1);
}
}
for (i = seg_st; i < seg_en; ++i) {
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2 changes: 1 addition & 1 deletion mmpriv.h
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);

void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, int is_hpc, mm128_v *p);

void mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]);
int mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]);
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag);
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs);
void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regs, const mm_reg1_t *const* regs, void *km, int opt_flag);
Expand Down