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r126: filter by fraction of seed coverage

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otherwise we may get too many poor overlap mappings.
This commit is contained in:
Heng Li
2017-06-30 22:15:45 -04:00
parent d73bb28097
commit 426c2975f6
6 changed files with 41 additions and 23 deletions
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main.c
+9 -7
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@@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r125-pre"
#define MM_VERSION "2.0-r126-pre"
void liftrlimit()
{
@@ -68,7 +68,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
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) {
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:D:", 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;
@@ -79,6 +79,7 @@ int main(int argc, char *argv[])
else if (c == 'v') mm_verbose = atoi(optarg);
else if (c == 'g') opt.max_gap = 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 == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
@@ -109,7 +110,7 @@ int main(int argc, char *argv[])
} 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;
opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f;
is_hpc = 1, k = 19, w = 5;
} else if (strcmp(optarg, "map10k") == 0) {
is_hpc = 1, k = 19;
@@ -140,11 +141,12 @@ int main(int argc, char *argv[])
fprintf(stderr, " -m INT minimal chaining score (matching bases minus log gap penalty) [%d]\n", opt.min_chain_score);
// fprintf(stderr, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres); // TODO: this option is never used; might be buggy
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, " -p FLOAT min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
fprintf(stderr, " -D FLOAT min fraction of seed matches [%g]\n", opt.min_seedcov_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, " map10k: -Hk19 (PacBio/ONT vs reference mapping)\n");
fprintf(stderr, " asm1m: -k19 -w19 (intra-species assembly to ref mapping)\n");
fprintf(stderr, " ava10k: -Hk19 -Sw5 -p0 -m100 -D.05 (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);