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Illumina Complete Long Read presets (#1069)

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* Implements a transition-aware alignment scoring scheme and configuration presets for ICLR

* Fix to enable use of general scoring matrix in ksw as suggested by lh3

---------

Co-authored-by: koadman <>
This commit is contained in:
Aaron Darling
2023-06-04 11:06:15 -04:00
committed by GitHub
co-authored by koadman
parent e28a55be86
commit ace990c381
5 changed files with 32 additions and 6 deletions
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options.c
+9
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@@ -45,6 +45,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->alt_drop = 0.15f;
opt->a = 2, opt->b = 4, opt->q = 4, opt->e = 2, opt->q2 = 24, opt->e2 = 1;
opt->transition = opt->b;
opt->sc_ambi = 1;
opt->zdrop = 400, opt->zdrop_inv = 200;
opt->end_bonus = -1;
@@ -112,6 +113,14 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->occ_dist = 500;
mo->min_mid_occ = 50, mo->max_mid_occ = 500;
mo->min_dp_max = 200;
} else if (strcmp(preset, "map-iclr-prerender") == 0) {
io->flag = 0, io->k = 15;
mo->b = 6, mo->transition = 1;
mo->q = 10, mo->q2 = 50;
} else if (strcmp(preset, "map-iclr") == 0) {
io->flag = 0, io->k = 19;
mo->b = 6, mo->transition = 4;
mo->q = 10, mo->q2 = 50;
} else if (strncmp(preset, "asm", 3) == 0) {
io->flag = 0, io->k = 19, io->w = 19;
mo->bw = 1000, mo->bw_long = 100000;