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r1118: use -r1k,100k for asm* modes

This commit is contained in:
Heng Li 2021-12-23 20:43:54 -05:00
parent c8f0a35c40
commit d3a89d34d4
3 changed files with 5 additions and 5 deletions
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2
main.c
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@ -7,7 +7,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.23-r1117-dirty"
#define MM_VERSION "2.23-r1118-dirty"
#ifdef __linux__
#include <sys/resource.h>

6
minimap2.1
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@ -565,7 +565,7 @@ Align older PacBio continuous long (CLR) reads to a reference genome
.B asm5
Long assembly to reference mapping
.RB ( -k19
.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
.BR -N50 ).
Typically, the alignment will not extend to regions with 5% or higher sequence
divergence. Only use this preset if the average divergence is far below 5%.
@ -573,14 +573,14 @@ divergence. Only use this preset if the average divergence is far below 5%.
.B asm10
Long assembly to reference mapping
.RB ( -k19
.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
.BR -N50 ).
Up to 10% sequence divergence.
.TP
.B asm20
Long assembly to reference mapping
.RB ( -k19
.B -w10 -U50,500 --rmq -r100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
.B -w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
.BR -N50 ).
Up to 20% sequence divergence.
.TP

2
options.c
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@ -113,7 +113,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->min_dp_max = 200;
} else if (strncmp(preset, "asm", 3) == 0) {
io->flag = 0, io->k = 19, io->w = 19;
mo->bw = mo->bw_long = 100000;
mo->bw = 1000, mo->bw_long = 100000;
mo->max_gap = 10000;
mo->flag |= MM_F_RMQ;
mo->min_mid_occ = 50, mo->max_mid_occ = 500;