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r940: added the splice:hq preset

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for high-quality CCS/mRNA splice alignment
This commit is contained in:
Heng Li
2019-05-04 14:00:31 -04:00
parent c2aec88b84
commit 6762368cf0
4 changed files with 13 additions and 5 deletions
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options.c
+3 -1
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@@ -120,7 +120,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->mid_occ = 1000;
mo->max_occ = 5000;
mo->mini_batch_size = 50000000;
} else if (strcmp(preset, "splice") == 0 || strcmp(preset, "cdna") == 0) {
} else if (strncmp(preset, "splice", 6) == 0 || strcmp(preset, "cdna") == 0) {
io->flag = 0, io->k = 15, io->w = 5;
mo->flag |= MM_F_SPLICE | MM_F_SPLICE_FOR | MM_F_SPLICE_REV | MM_F_SPLICE_FLANK;
mo->max_gap = 2000, mo->max_gap_ref = mo->bw = 200000;
@@ -128,6 +128,8 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->noncan = 9;
mo->junc_bonus = 9;
mo->zdrop = 200, mo->zdrop_inv = 100; // because mo->a is halved
if (strcmp(preset, "splice:hq") == 0)
mo->junc_bonus = 5, mo->b = 4, mo->q = 6, mo->q2 = 24;
} else return -1;
return 0;
}