From e2dbfe60e38082c1d11856c5272f9387a3dee377 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 23 Feb 2021 10:43:41 -0500 Subject: [PATCH] output more memory information --- bwamem.c | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/bwamem.c b/bwamem.c index 104d0c9..859aff4 100644 --- a/bwamem.c +++ b/bwamem.c @@ -1205,11 +1205,13 @@ static void worker1(void *data, int i, int tid) if (!(w->opt->flag&MEM_F_PE)) { if (bwa_verbose >= 4) printf("=====> Processing read '%s' <=====\n", w->seqs[i].name); w->regs[i] = mem_align1_core(w->opt, w->bwt, w->bns, w->pac, w->seqs[i].l_seq, w->seqs[i].seq, w->aux[tid]); + fprintf(stderr, "Q1\t%s\t%.3f\t%d\n", w->seqs[i].name, peakrss() / 1073741824.0, tid); } else { if (bwa_verbose >= 4) printf("=====> Processing read '%s'/1 <=====\n", w->seqs[i<<1|0].name); w->regs[i<<1|0] = mem_align1_core(w->opt, w->bwt, w->bns, w->pac, w->seqs[i<<1|0].l_seq, w->seqs[i<<1|0].seq, w->aux[tid]); if (bwa_verbose >= 4) printf("=====> Processing read '%s'/2 <=====\n", w->seqs[i<<1|1].name); w->regs[i<<1|1] = mem_align1_core(w->opt, w->bwt, w->bns, w->pac, w->seqs[i<<1|1].l_seq, w->seqs[i<<1|1].seq, w->aux[tid]); + fprintf(stderr, "Q1\t%s\t%.3f\t%d\n", w->seqs[i<<1|0].name, peakrss() / 1073741824.0, tid); } } @@ -1223,12 +1225,12 @@ static void worker2(void *data, int i, int tid) mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a, w->n_processed + i); if (w->opt->flag & MEM_F_PRIMARY5) mem_reorder_primary5(w->opt->T, &w->regs[i]); mem_reg2sam(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0); - fprintf(stderr, "Q\t%s\t%.3f\n", w->seqs[i].name, peakrss() / 1073741824.0); + fprintf(stderr, "Q2\t%s\t%.3f\n", w->seqs[i].name, peakrss() / 1073741824.0); free(w->regs[i].a); } else { if (bwa_verbose >= 4) printf("=====> Finalizing read pair '%s' <=====\n", w->seqs[i<<1|0].name); mem_sam_pe(w->opt, w->bns, w->pac, w->pes, (w->n_processed>>1) + i, &w->seqs[i<<1], &w->regs[i<<1]); - fprintf(stderr, "Q\t%s\t%.3f\n", w->seqs[i<<1|0].name, peakrss() / 1073741824.0); + fprintf(stderr, "Q2\t%s\t%.3f\n", w->seqs[i<<1|0].name, peakrss() / 1073741824.0); free(w->regs[i<<1|0].a); free(w->regs[i<<1|1].a); } }