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r176: removed seedcov_ratio; changed default opt

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min_seedcov_ratio is not used
This commit is contained in:
Heng Li
2017-07-12 12:47:46 -04:00
parent 52caf79395
commit b4280d186f
5 changed files with 26 additions and 29 deletions
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main.c
+11 -10
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@@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r175-pre"
#define MM_VERSION "2.0-r176-pre"
void liftrlimit()
{
@@ -43,7 +43,7 @@ static int test_idx(const char *fn)
static struct option long_options[] = {
{ "bucket-bits", required_argument, 0, 0 },
{ "mb-size", required_argument, 0, 0 },
{ "mb-size", required_argument, 0, 'K' },
{ "int-rname", no_argument, 0, 0 },
{ "no-kalloc", no_argument, 0, 0 },
{ "print-qname", no_argument, 0, 0 },
@@ -73,7 +73,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
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) {
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) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'H') is_hpc = 1;
@@ -85,7 +85,6 @@ int main(int argc, char *argv[])
else if (c == 'g') opt.max_gap = atoi(optarg);
else if (c == 'N') opt.best_n = atoi(optarg);
else if (c == 'p') opt.pri_ratio = atof(optarg);
else if (c == 'D') opt.min_seedcov_ratio = atof(optarg);
else if (c == 'M') opt.mask_level = atof(optarg);
else if (c == 'c') opt.flag |= MM_F_CIGAR;
else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
@@ -114,7 +113,7 @@ int main(int argc, char *argv[])
} else if (c == 'E') {
opt.e = opt.e2 = strtol(optarg, &s, 10);
if (*s == ',') opt.e2 = strtol(s + 1, &s, 10);
} else if (c == 'I' || (c == 0 && long_idx == 1)) {
} else if (c == 'I' || c == 'K') {
double x;
char *p;
x = strtod(optarg, &p);
@@ -126,11 +125,13 @@ int main(int argc, char *argv[])
} else if (c == 'x') {
if (strcmp(optarg, "ava-ont") == 0) {
opt.flag |= MM_F_AVA | MM_F_NO_SELF;
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;
opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.max_gap = 10000, opt.max_chain_skip = 25;
minibatch_size = 500000000;
k = 15, w = 5;
} else if (strcmp(optarg, "ava-pb") == 0) {
opt.flag |= MM_F_AVA | MM_F_NO_SELF;
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;
opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.max_gap = 10000, opt.max_chain_skip = 25;
minibatch_size = 500000000;
is_hpc = 1, k = 19, w = 5;
} else if (strcmp(optarg, "map10k") == 0) {
is_hpc = 1, k = 19;
@@ -163,10 +164,9 @@ int main(int argc, char *argv[])
fprintf(stderr, " -X skip self and dual mappings (for the all-vs-all mode)\n");
fprintf(stderr, " -p FLOAT min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
fprintf(stderr, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n);
fprintf(stderr, " -D FLOAT min fraction of minimizer matches [%g]\n", opt.min_seedcov_ratio);
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -D.05 -g10000 --max-chain-skip 25 (PacBio read overlap)\n");
fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -D.05 -g10000 --max-chain-skip 25 (ONT read overlap)\n");
fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n");
fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n");
fprintf(stderr, " map10k: -Hk19 (PacBio/ONT vs reference mapping)\n");
fprintf(stderr, " asm1m: -k19 -w19 (intra-species assembly to ref mapping)\n");
fprintf(stderr, " Alignment:\n");
@@ -181,6 +181,7 @@ int main(int argc, char *argv[])
fprintf(stderr, " -a output in the SAM format (PAF by default)\n");
fprintf(stderr, " -c output CIGAR in PAF\n");
fprintf(stderr, " -t INT number of threads [%d]\n", n_threads);
fprintf(stderr, " -K NUM minibatch size [200M]\n");
// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose);
fprintf(stderr, " -V show version number\n");
fprintf(stderr, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n");