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r490: improved short-read extension heuristic

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Now we find the best scoring ungapped seeded segment and then extend from it.
There is no gap filling for short reads.
This commit is contained in:
Heng Li
2017-10-08 21:36:34 -04:00
parent f9415628a8
commit 9fea4d16b3
3 changed files with 93 additions and 46 deletions
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map.c
+2 -1
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@@ -83,8 +83,9 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->flag |= MM_F_SR | MM_F_FRAG_MODE | MM_F_NO_PRINT_2ND;
mo->pe_ori = 0<<1|1; // FR
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 32, mo->e2 = 1;
mo->zdrop = 100;
mo->max_frag_len = 800;
mo->max_gap = 200;
mo->max_gap = 100;
mo->bw = 100;
mo->pri_ratio = 0.5f;
mo->min_cnt = 2;