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r123: fixed a mem leak; more presets

This commit is contained in:
Heng Li 2017-06-30 15:39:05 -04:00
parent 646a746cdc
commit 3a5486325a
2 changed files with 13 additions and 2 deletions
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1
hit.c
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@ -141,6 +141,7 @@ void mm_select_sub(void *km, float mask_level, float pri_ratio, int *n_, mm_reg1
for (i = k = 0; i < n; ++i)
if (r[i].parent == i || r[i].score >= r[r[i].parent].score * pri_ratio)
r[k++] = r[i];
else if (r[i].p) free(r[i].p);
if (k != n) mm_sync_regs(km, k, r); // removing hits requires sync()
*n_ = k;
}

14
main.c
View File

@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r122-pre"
#define MM_VERSION "2.0-r123-pre"
void liftrlimit()
{
@ -109,13 +109,21 @@ int main(int argc, char *argv[])
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 0;
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) {
is_hpc = 1, k = 19;
} else {
fprintf(stderr, "[E::%s] unknown preset '%s'\n", __func__, optarg);
return 1;
}
}
}
@ -141,6 +149,8 @@ int main(int argc, char *argv[])
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, " Alignment:\n");
fprintf(stderr, " -A INT matching score [%d]\n", opt.a);
fprintf(stderr, " -B INT mismatch penalty [%d]\n", opt.b);