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r1028: backport minigraph -U

This commit is contained in:
Heng Li 2021-05-01 15:41:39 -04:00
parent e8823a3709
commit 0f5608c4a4
4 changed files with 11 additions and 5 deletions
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7
main.c
View File

@ -7,7 +7,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.18-r1027-dirty" #define MM_VERSION "2.18-r1028-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>
@ -108,7 +108,7 @@ static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const cha
int main(int argc, char *argv[]) int main(int argc, char *argv[])
{ {
const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:e:"; const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:e:U:";
ketopt_t o = KETOPT_INIT; ketopt_t o = KETOPT_INIT;
mm_mapopt_t opt; mm_mapopt_t opt;
mm_idxopt_t ipt; mm_idxopt_t ipt;
@ -248,6 +248,9 @@ int main(int argc, char *argv[])
} else if (c == 'V') { } else if (c == 'V') {
puts(MM_VERSION); puts(MM_VERSION);
return 0; return 0;
} else if (c == 'U') {
opt.min_mid_occ = strtol(o.arg, &s, 10);
if (*s == ',') opt.max_mid_occ = strtol(s + 1, &s, 10);
} else if (c == 'f') { } else if (c == 'f') {
double x; double x;
char *p; char *p;

2
minimap.h
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@ -146,7 +146,7 @@ typedef struct {
int pe_ori, pe_bonus; int pe_ori, pe_bonus;
float mid_occ_frac; // only used by mm_mapopt_update(); see below float mid_occ_frac; // only used by mm_mapopt_update(); see below
int32_t min_mid_occ; int32_t min_mid_occ, max_mid_occ;
int32_t mid_occ; // ignore seeds with occurrences above this threshold int32_t mid_occ; // ignore seeds with occurrences above this threshold
int32_t max_occ, max_max_occ, occ_dist; int32_t max_occ, max_max_occ, occ_dist;
int64_t mini_batch_size; // size of a batch of query bases to process in parallel int64_t mini_batch_size; // size of a batch of query bases to process in parallel

2
minimap2.1
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@ -540,7 +540,7 @@ is determined by the sequencing error mode.
PacBio HiFi reads to reference mapping PacBio HiFi reads to reference mapping
.RB ( -k19 .RB ( -k19
.B -w10 -A1 -B4 -O6,26 -E2,1 -s200 -e100 -g10k .B -w10 -A1 -B4 -O6,26 -E2,1 -s200 -e100 -g10k
.BR --min-occ-floor=100 ). .BR -U100,500 ).
.TP .TP
.B asm5 .B asm5
Long assembly to reference mapping Long assembly to reference mapping

5
options.c
View File

@ -16,6 +16,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
memset(opt, 0, sizeof(mm_mapopt_t)); memset(opt, 0, sizeof(mm_mapopt_t));
opt->seed = 11; opt->seed = 11;
opt->mid_occ_frac = 2e-4f; opt->mid_occ_frac = 2e-4f;
opt->max_mid_occ = 1000000000;
opt->sdust_thres = 0; // no SDUST masking opt->sdust_thres = 0; // no SDUST masking
opt->min_cnt = 3; opt->min_cnt = 3;
@ -63,6 +64,8 @@ void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
opt->mid_occ = mm_idx_cal_max_occ(mi, opt->mid_occ_frac); opt->mid_occ = mm_idx_cal_max_occ(mi, opt->mid_occ_frac);
if (opt->mid_occ < opt->min_mid_occ) if (opt->mid_occ < opt->min_mid_occ)
opt->mid_occ = opt->min_mid_occ; opt->mid_occ = opt->min_mid_occ;
if (opt->max_mid_occ > opt->min_mid_occ && opt->mid_occ > opt->max_mid_occ)
opt->mid_occ = opt->max_mid_occ;
if (mm_verbose >= 3) if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] mid_occ = %d\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), opt->mid_occ); fprintf(stderr, "[M::%s::%.3f*%.2f] mid_occ = %d\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), opt->mid_occ);
} }
@ -96,7 +99,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->a = 1, mo->b = 4, mo->q = 6, mo->q2 = 26, mo->e = 2, mo->e2 = 1; mo->a = 1, mo->b = 4, mo->q = 6, mo->q2 = 26, mo->e = 2, mo->e2 = 1;
mo->max_gap = 10000; mo->max_gap = 10000;
mo->occ_dist = 500; mo->occ_dist = 500;
mo->min_mid_occ = 100; mo->min_mid_occ = 100, mo->max_mid_occ = 500;
mo->min_dp_max = 200; mo->min_dp_max = 200;
} else if (strcmp(preset, "asm5") == 0) { } else if (strcmp(preset, "asm5") == 0) {
io->flag = 0, io->k = 19, io->w = 19; io->flag = 0, io->k = 19, io->w = 19;