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r125: changed CLI options

This commit is contained in:
Heng Li 2017-06-30 19:08:47 -04:00
parent b08591c7a0
commit d73bb28097
1 changed files with 11 additions and 17 deletions
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28
main.c
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@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r124-pre"
#define MM_VERSION "2.0-r125-pre"
void liftrlimit()
{
@ -50,6 +50,7 @@ static struct option long_options[] = {
{ "min-chain-score",required_argument, 0, 'm' },
{ "mask-level", required_argument, 0, 'M' },
{ "min-dp-score", required_argument, 0, 's' },
{ "sam", no_argument, 0, 'b' },
{ 0, 0, 0, 0}
};
@ -67,7 +68,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt_long(argc, argv, "w:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:F:A:B:O:E:m:", long_options, &long_idx)) >= 0) {
while ((c = getopt_long(argc, argv, "bw:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:A:B:O:E:m:", 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;
@ -81,6 +82,7 @@ int main(int argc, char *argv[])
else if (c == 'M') opt.mask_level = atof(optarg);
else if (c == 'c') opt.flag |= MM_F_CIGAR;
else if (c == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
else if (c == 'b') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
else if (c == 'T') opt.sdust_thres = atoi(optarg);
else if (c == 'n') opt.min_cnt = atoi(optarg);
else if (c == 'm') opt.min_chain_score = atoi(optarg);
@ -104,23 +106,15 @@ int main(int argc, char *argv[])
else if (*p == 'K' || *p == 'k') x *= 1e3;
if (c == 'I') batch_size = (uint64_t)(x + .499);
else minibatch_size = (uint64_t)(x + .499);
} else if (c == 'F') {
if (strcmp(optarg, "sam") == 0) opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
else if (strcmp(optarg, "paf") == 0) opt.flag &= ~MM_F_OUT_SAM;
else {
fprintf(stderr, "[E::%s] unknown output format '%s'\n", __func__, optarg);
return 1;
}
} else if (c == 'x') {
if (strcmp(optarg, "ava10k") == 0) {
opt.flag |= MM_F_AVA | MM_F_NO_SELF;
opt.min_chain_score = 100, opt.pri_ratio = 0.0f;
is_hpc = 1, k = 19, w = 5;
} else if (strcmp(optarg, "sam10k") == 0) {
opt.flag = MM_F_OUT_SAM | MM_F_CIGAR;
is_hpc = 1, k = 19;
} else if (strcmp(optarg, "paf10k") == 0) {
} else if (strcmp(optarg, "map10k") == 0) {
is_hpc = 1, k = 19;
} else if (strcmp(optarg, "asm1m") == 0) {
k = 19, w = 19;
} else {
fprintf(stderr, "[E::%s] unknown preset '%s'\n", __func__, optarg);
return 1;
@ -148,9 +142,9 @@ int main(int argc, char *argv[])
fprintf(stderr, " -S skip self and dual mappings (for the all-vs-all mode)\n");
fprintf(stderr, " -p FLOAT threshold to output a mapping [%g]\n", opt.pri_ratio);
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
fprintf(stderr, " ava10k: -Hk19 -Sw5 -p0 -m100 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " sam10k: -Hk19 -Fsam (PacBio/ONT vs reference alignment)\n");
fprintf(stderr, " paf10k: -Hk19 (PacBio/ONT vs reference mapping/alignment)\n");
fprintf(stderr, " ava10k: -Hk19 -Sw5 -p0 -m100 (PacBio/ONT all-vs-all read mapping)\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");
fprintf(stderr, " -A INT matching score [%d]\n", opt.a);
fprintf(stderr, " -B INT mismatch penalty [%d]\n", opt.b);
@ -159,7 +153,7 @@ int main(int argc, char *argv[])
fprintf(stderr, " -z INT Z-drop score [%d]\n", opt.zdrop);
fprintf(stderr, " -s INT minimal peak DP alignment score [%d]\n", opt.min_dp_max);
fprintf(stderr, " Input/Output:\n");
fprintf(stderr, " -F STR output format: sam or paf [paf]\n");
fprintf(stderr, " -b 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, " -v INT verbose level [%d]\n", mm_verbose);