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dev-r1076: log gap penalty

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Heng Li
2021-07-17 18:23:59 -04:00
parent 52fafe0fed
commit 2546999639
5 changed files with 27 additions and 20 deletions
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main.c
+5 -2
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@@ -7,7 +7,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.21-r1074-qs-dirty"
#define MM_VERSION "2.21-dev-r1076-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -73,6 +73,7 @@ static ko_longopt_t long_options[] = {
{ "mask-len", ko_required_argument, 346 },
{ "rmq", ko_optional_argument, 347 },
{ "qstrand", ko_no_argument, 348 },
{ "log-gap", ko_required_argument, 349 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
@@ -101,7 +102,7 @@ static inline int64_t mm_parse_num(const char *str)
return mm_parse_num2(str, 0);
}
static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const char *arg, int yes_to_set)
static inline void yes_or_no(mm_mapopt_t *opt, int64_t flag, int long_idx, const char *arg, int yes_to_set)
{
if (yes_to_set) {
if (strcmp(arg, "yes") == 0 || strcmp(arg, "y") == 0) opt->flag |= flag;
@@ -252,6 +253,8 @@ int main(int argc, char *argv[])
yes_or_no(&opt, MM_F_NO_DUAL, o.longidx, o.arg, 0);
} else if (c == 347) { // --rmq
yes_or_no(&opt, MM_F_RMQ, o.longidx, o.arg, 1);
} else if (c == 349) { // --log-gap
yes_or_no(&opt, MM_F_NO_LOG_GAP, o.longidx, o.arg, 0);
} else if (c == 'S') {
opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
if (mm_verbose >= 2)