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Removed the debug output; resolves #320

This commit is contained in:
Heng Li 2021-03-09 08:56:52 -05:00
parent 5b96937edc
commit ddbd5f7fb7
1 changed files with 0 additions and 4 deletions
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4
bwamem.c
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@ -1205,13 +1205,11 @@ static void worker1(void *data, int i, int tid)
if (!(w->opt->flag&MEM_F_PE)) { if (!(w->opt->flag&MEM_F_PE)) {
if (bwa_verbose >= 4) printf("=====> Processing read '%s' <=====\n", w->seqs[i].name); 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]); 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 { } else {
if (bwa_verbose >= 4) printf("=====> Processing read '%s'/1 <=====\n", w->seqs[i<<1|0].name); 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]); 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); 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]); 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);
} }
} }
@ -1225,12 +1223,10 @@ 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); 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]); 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); mem_reg2sam(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
fprintf(stderr, "Q2\t%s\t%.3f\n", w->seqs[i].name, peakrss() / 1073741824.0);
free(w->regs[i].a); free(w->regs[i].a);
} else { } else {
if (bwa_verbose >= 4) printf("=====> Finalizing read pair '%s' <=====\n", w->seqs[i<<1|0].name); 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]); 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, "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); free(w->regs[i<<1|0].a); free(w->regs[i<<1|1].a);
} }
} }