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r626: function to check incorrect scoring system

This commit is contained in:
Heng Li 2017-12-13 12:23:43 -05:00
parent d003a00d71
commit ab345e600b
3 changed files with 19 additions and 1 deletions
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4
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "getopt.h" #include "getopt.h"
#define MM_VERSION "2.6-r625-dirty" #define MM_VERSION "2.6-r626-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>
@ -202,6 +202,8 @@ int main(int argc, char *argv[])
} }
if (!fnw && !(opt.flag&MM_F_CIGAR)) if (!fnw && !(opt.flag&MM_F_CIGAR))
ipt.flag |= MM_I_NO_SEQ; ipt.flag |= MM_I_NO_SEQ;
if (mm_check_opt(&ipt, &opt) < 0)
return 1;
if (argc == optind || fp_help == stdout) { if (argc == optind || fp_help == stdout) {
fprintf(fp_help, "Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]\n"); fprintf(fp_help, "Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]\n");

15
map.c
View File

@ -115,6 +115,21 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
return 0; return 0;
} }
int mm_check_opt(const mm_idxopt_t *io, const mm_mapopt_t *mo)
{
if (mo->a + 2 * (mo->q + mo->e) > 127 || mo->a + 2 * (mo->q2 + mo->e2) > 127) {
if (mm_verbose >= 1)
fprintf(stderr, "[ERROR]\033[1;31m scoring system violating {-A}+2*({-O}+{-E}) <= 127\033[0m\n");
return -1;
}
if ((mo->q != mo->q2 || mo->e != mo->e2) && !(mo->e > mo->e2 && mo->q + mo->e < mo->q2 + mo->e2)) {
if (mm_verbose >= 1)
fprintf(stderr, "[ERROR]\033[1;31m dual gap penalties violating E1>E2 and O1+E1<O2+E2\033[0m\n");
return -2;
}
return 0;
}
typedef struct { typedef struct {
uint32_t n; uint32_t n;
uint32_t qpos; uint32_t qpos;

1
minimap.h
View File

@ -155,6 +155,7 @@ extern double mm_realtime0; // wall-clock timer
* @return 0 if success; -1 if _present_ unknown * @return 0 if success; -1 if _present_ unknown
*/ */
int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo); int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo);
int mm_check_opt(const mm_idxopt_t *io, const mm_mapopt_t *mo);
/** /**
* Update mm_mapopt_t::mid_occ via mm_mapopt_t::mid_occ_frac * Update mm_mapopt_t::mid_occ via mm_mapopt_t::mid_occ_frac