From 3afcdc7746fa8a4656df7ef4cbbe24a855f87ffb Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 30 Dec 2013 16:05:43 -0500 Subject: [PATCH] debugging code only: print seeds --- bwamem.c | 1 + 1 file changed, 1 insertion(+) diff --git a/bwamem.c b/bwamem.c index 9ab22e3..a609e0d 100644 --- a/bwamem.c +++ b/bwamem.c @@ -215,6 +215,7 @@ static void mem_insert_seed(const mem_opt_t *opt, int64_t l_pac, kbtree_t(chn) * s.rbeg = tmp.pos = bwt_sa(itr->bwt, p->x[0] + k); // this is the base coordinate in the forward-reverse reference s.qbeg = p->info>>32; s.len = slen; + if (bwa_verbose >= 5) printf("SEED l=%d,qb=%d,rb=%ld\n", s.len, s.qbeg, (long)s.rbeg); if (s.rbeg < l_pac && l_pac < s.rbeg + s.len) continue; // bridging forward-reverse boundary; skip if (kb_size(tree)) { kb_intervalp(chn, tree, &tmp, &lower, &upper); // find the closest chain