r176: removed seedcov_ratio; changed default opt
min_seedcov_ratio is not used
This commit is contained in:
Heng Li
parent
52caf79395
commit
b4280d186f
4
hit.c
4
hit.c
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@ -197,10 +197,6 @@ void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *re
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mm_reg1_t *r = ®s[i];
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int flt = 0;
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if (r->cnt < opt->min_cnt) flt = 1;
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else {
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int blen = r->qe - r->qs < r->re - r->rs? r->qe - r->qs : r->re - r->rs;
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if (r->score < blen * opt->min_seedcov_ratio * opt->a) flt = 1;
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}
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if (r->p) {
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if (r->p->blen - r->p->n_ambi - r->p->n_diff < opt->min_chain_score) flt = 1;
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else if (r->p->dp_max < opt->min_dp_max) flt = 1;
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21
main.c
21
main.c
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@ -10,7 +10,7 @@
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#include "minimap.h"
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#include "mmpriv.h"
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#define MM_VERSION "2.0-r175-pre"
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#define MM_VERSION "2.0-r176-pre"
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void liftrlimit()
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{
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@ -43,7 +43,7 @@ static int test_idx(const char *fn)
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static struct option long_options[] = {
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{ "bucket-bits", required_argument, 0, 0 },
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{ "mb-size", required_argument, 0, 0 },
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{ "mb-size", required_argument, 0, 'K' },
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{ "int-rname", no_argument, 0, 0 },
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{ "no-kalloc", no_argument, 0, 0 },
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{ "print-qname", no_argument, 0, 0 },
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@ -73,7 +73,7 @@ int main(int argc, char *argv[])
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mm_realtime0 = realtime();
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mm_mapopt_init(&opt);
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while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:D:N:Q", long_options, &long_idx)) >= 0) {
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while ((c = getopt_long(argc, argv, "aw:k:K:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Q", long_options, &long_idx)) >= 0) {
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if (c == 'w') w = atoi(optarg);
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else if (c == 'k') k = atoi(optarg);
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else if (c == 'H') is_hpc = 1;
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@ -85,7 +85,6 @@ int main(int argc, char *argv[])
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else if (c == 'g') opt.max_gap = atoi(optarg);
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else if (c == 'N') opt.best_n = atoi(optarg);
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else if (c == 'p') opt.pri_ratio = atof(optarg);
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else if (c == 'D') opt.min_seedcov_ratio = atof(optarg);
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else if (c == 'M') opt.mask_level = atof(optarg);
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else if (c == 'c') opt.flag |= MM_F_CIGAR;
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else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
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@ -114,7 +113,7 @@ int main(int argc, char *argv[])
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} else if (c == 'E') {
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opt.e = opt.e2 = strtol(optarg, &s, 10);
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if (*s == ',') opt.e2 = strtol(s + 1, &s, 10);
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} else if (c == 'I' || (c == 0 && long_idx == 1)) {
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} else if (c == 'I' || c == 'K') {
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double x;
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char *p;
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x = strtod(optarg, &p);
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@ -126,11 +125,13 @@ int main(int argc, char *argv[])
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} else if (c == 'x') {
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if (strcmp(optarg, "ava-ont") == 0) {
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opt.flag |= MM_F_AVA | MM_F_NO_SELF;
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opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000, opt.max_chain_skip = 25;
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opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.max_gap = 10000, opt.max_chain_skip = 25;
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minibatch_size = 500000000;
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k = 15, w = 5;
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} else if (strcmp(optarg, "ava-pb") == 0) {
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opt.flag |= MM_F_AVA | MM_F_NO_SELF;
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opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000, opt.max_chain_skip = 25;
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opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.max_gap = 10000, opt.max_chain_skip = 25;
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minibatch_size = 500000000;
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is_hpc = 1, k = 19, w = 5;
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} else if (strcmp(optarg, "map10k") == 0) {
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is_hpc = 1, k = 19;
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@ -163,10 +164,9 @@ int main(int argc, char *argv[])
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fprintf(stderr, " -X skip self and dual mappings (for the all-vs-all mode)\n");
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fprintf(stderr, " -p FLOAT min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
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fprintf(stderr, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n);
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fprintf(stderr, " -D FLOAT min fraction of minimizer matches [%g]\n", opt.min_seedcov_ratio);
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fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
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fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -D.05 -g10000 --max-chain-skip 25 (PacBio read overlap)\n");
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fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -D.05 -g10000 --max-chain-skip 25 (ONT read overlap)\n");
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fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n");
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fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n");
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fprintf(stderr, " map10k: -Hk19 (PacBio/ONT vs reference mapping)\n");
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fprintf(stderr, " asm1m: -k19 -w19 (intra-species assembly to ref mapping)\n");
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fprintf(stderr, " Alignment:\n");
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@ -181,6 +181,7 @@ int main(int argc, char *argv[])
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fprintf(stderr, " -a output in the SAM format (PAF by default)\n");
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fprintf(stderr, " -c output CIGAR in PAF\n");
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fprintf(stderr, " -t INT number of threads [%d]\n", n_threads);
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fprintf(stderr, " -K NUM minibatch size [200M]\n");
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// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose);
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fprintf(stderr, " -V show version number\n");
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fprintf(stderr, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n");
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1
map.c
1
map.c
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@ -20,7 +20,6 @@ void mm_mapopt_init(mm_mapopt_t *opt)
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opt->bw = 500;
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opt->max_gap = 5000;
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opt->max_chain_skip = 25;
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opt->min_seedcov_ratio = 0.0f;
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opt->mask_level = 0.5f;
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opt->pri_ratio = 0.8f;
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@ -77,7 +77,6 @@ typedef struct {
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int max_chain_skip;
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int min_cnt;
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int min_chain_score;
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float min_seedcov_ratio;
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float mask_level;
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float pri_ratio;
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28
minimap2.1
28
minimap2.1
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@ -164,12 +164,6 @@ secondary alignments [5]. This option has no effect when
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.B -X
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is applied.
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.TP
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.BI -D \ FLOAT
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Discard a chain if the fraction of matching bases over the length of
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query/target sequences in the chain is
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.RI < FLOAT
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[0].
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.TP
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.BI -x \ STR
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Preset []. This option applies multiple options at the same time. It should be
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applied before other options because options applied later will overwrite the
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@ -181,10 +175,10 @@ are:
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.RS
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.TP 8
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.B ava-pb
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PacBio all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -D.05 -g10000)
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PacBio all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip 25)
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.TP 8
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.B ava-ont
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Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -D.05 -g10000)
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Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip 25)
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.TP
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.B map10k
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PacBio/Oxford Nanopore read to reference mapping (-Hk19)
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@ -249,14 +243,22 @@ sequences, and uses up to
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threads when mapping (the extra thread is for I/O, which is frequently idle and
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takes little CPU time).
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.TP
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.B -V
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Print version number to stdout
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.TP
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.BI --mb-size \ STR
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.BI -K \ NUM
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Number of bases loaded into memory to process in a mini-batch [200M].
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Similar to option
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.BR -I ,
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K/M/G/k/m/g suffix is accepted. This option affects both indexing and mapping.
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K/M/G/k/m/g suffix is accepted. A large
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.I NUM
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helps load balancing in the multi-threading mode, at the cost of increased
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memory. Preset
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.B ava-pb
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and
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.B ava-ont
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use
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.BR -K500m .
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.TP
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.B -V
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Print version number to stdout
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.SS Miscellaneous options
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.TP 10
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.B --no-kalloc
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