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r436: working on short reads

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The result is mixed - lots of room for tuning
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Heng Li
2017-09-25 14:06:29 -04:00
parent 3bb66e1ed3
commit 81008dd371
2 changed files with 16 additions and 11 deletions
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map.c
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@@ -78,6 +78,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->flag |= MM_F_SR | MM_F_MULTI_SEG | MM_F_SEG_REV;
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 32, mo->e2 = 1;
mo->max_gap = 100;
mo->max_gap_ref = 1000;
mo->pri_ratio = 0.5f;
mo->min_cnt = 2;
mo->min_chain_score = 20;