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r159: use two-piece gap penalty

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Heng Li
2017-07-08 10:26:00 -04:00
parent 9823317e8f
commit cc554aee43
9 changed files with 499 additions and 113 deletions
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map.c
+2 -2
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@@ -30,8 +30,8 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->max_join_short = 2000;
opt->min_join_flank_sc = 1000;
opt->a = 1, opt->b = 2, opt->q = 2, opt->e = 1;
opt->zdrop = 200;
opt->a = 2, opt->b = 4, opt->q = 4, opt->e = 2, opt->q2 = 24, opt->e2 = 1;
opt->zdrop = 400;
opt->min_dp_max = opt->min_chain_score;
opt->min_ksw_len = 100;
}