diff --git a/main.c b/main.c index 1dae0ac..160801f 100644 --- a/main.c +++ b/main.c @@ -7,7 +7,7 @@ #include "mmpriv.h" #include "ketopt.h" -#define MM_VERSION "2.18-r1026-dirty" +#define MM_VERSION "2.18-r1027-dirty" #ifdef __linux__ #include diff --git a/minimap2.1 b/minimap2.1 index f132780..018d958 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -523,7 +523,7 @@ Available .I STR are: .RS -.TP 8 +.TP 9 .B map-pb PacBio/Oxford Nanopore read to reference mapping .RB ( -Hk19 ) @@ -536,6 +536,12 @@ more sensitive results in comparison to normal minimizers. For Oxford Nanopore data, normal minimizers are better, though not much. The effectiveness of HPC is determined by the sequencing error mode. .TP +.B map-hifi +PacBio HiFi reads to reference mapping +.RB ( -k19 +.B -w10 -A1 -B4 -O6,26 -E2,1 -s200 -e100 -g10k +.BR --min-occ-floor=100 ). +.TP .B asm5 Long assembly to reference mapping .RB ( -k19 diff --git a/options.c b/options.c index 45212dd..a597962 100644 --- a/options.c +++ b/options.c @@ -91,10 +91,11 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo) io->flag |= MM_I_HPC, io->k = 19; } else if (strcmp(preset, "map-ont") == 0) { io->flag = 0, io->k = 15; - } else if (strcmp(preset, "hifi") == 0 || strcmp(preset, "ccs") == 0) { + } else if (strcmp(preset, "map-hifi") == 0 || strcmp(preset, "map-ccs") == 0) { io->flag = 0, io->k = 19, io->w = 19; mo->a = 1, mo->b = 4, mo->q = 6, mo->q2 = 26, mo->e = 2, mo->e2 = 1; - mo->occ_dist = 100; + mo->max_gap = 10000; + mo->occ_dist = 500; mo->min_mid_occ = 100; mo->min_dp_max = 200; } else if (strcmp(preset, "asm5") == 0) {