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r1112: added --print-chains for debugging

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Heng Li
2021-11-18 21:26:41 -05:00
parent d0cff3eb36
commit b276772890
3 changed files with 5 additions and 2 deletions
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map.c
+1 -1
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@@ -328,7 +328,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
mm_hit_sort(b->km, &n_regs0, regs0, opt->alt_drop); // this step can be merged into mm_gen_regs(); will do if this shows up in profile
}
if (mm_dbg_flag & MM_DBG_PRINT_SEED)
if (mm_dbg_flag & (MM_DBG_PRINT_SEED|MM_DBG_PRINT_CHAIN))
for (j = 0; j < n_regs0; ++j)
for (i = regs0[j].as; i < regs0[j].as + regs0[j].cnt; ++i)
fprintf(stderr, "CN\t%d\t%s\t%d\t%c\t%d\t%d\t%d\n", j, mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, "+-"[a[i].x>>63], (int32_t)a[i].y, (int32_t)(a[i].y>>32&0xff),