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r1027: renamed hifi to map-hifi; changed default

This commit is contained in:
Heng Li 2021-05-01 15:22:51 -04:00
parent 7edeec67b0
commit e8823a3709
3 changed files with 11 additions and 4 deletions
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2
main.c
View File

@ -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 <sys/resource.h>

8
minimap2.1
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@ -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

5
options.c
View File

@ -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) {