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r1090: log wall-clock time for each read

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Heng Li
2021-08-04 17:45:09 -04:00
parent 2392e54fe2
commit 5180b70ff3
2 changed files with 7 additions and 2 deletions
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map.c
+6 -1
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@@ -410,10 +410,13 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
step_t *s = (step_t*)_data;
int qlens[MM_MAX_SEG], j, off = s->seg_off[i], pe_ori = s->p->opt->pe_ori;
const char *qseqs[MM_MAX_SEG];
double t = 0.0;
mm_tbuf_t *b = s->buf[tid];
assert(s->n_seg[i] <= MM_MAX_SEG);
if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
if (mm_dbg_flag & MM_DBG_PRINT_QNAME) {
fprintf(stderr, "QR\t%s\t%d\t%d\n", s->seq[off].name, tid, s->seq[off].l_seq);
t = realtime();
}
for (j = 0; j < s->n_seg[i]; ++j) {
if (s->n_seg[i] == 2 && ((j == 0 && (pe_ori>>1&1)) || (j == 1 && (pe_ori&1))))
mm_revcomp_bseq(&s->seq[off + j]);
@@ -445,6 +448,8 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
r->rev = !r->rev;
}
}
if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
fprintf(stderr, "QT\t%s\t%d\t%.6f\n", s->seq[off].name, tid, realtime() - t);
}
static void merge_hits(step_t *s)