From 5180b70ff3082dbfadca9d5de44152b9e825b0c0 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 4 Aug 2021 17:45:09 -0400 Subject: [PATCH] r1090: log wall-clock time for each read --- main.c | 2 +- map.c | 7 ++++++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/main.c b/main.c index b3d2e80..81a6980 100644 --- a/main.c +++ b/main.c @@ -7,7 +7,7 @@ #include "mmpriv.h" #include "ketopt.h" -#define MM_VERSION "2.21-dev-r1089-dirty" +#define MM_VERSION "2.21-dev-r1090-dirty" #ifdef __linux__ #include diff --git a/map.c b/map.c index 15d1b7b..f03b7ea 100644 --- a/map.c +++ b/map.c @@ -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)