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r160: -O and -E accept two numbers

This commit is contained in:
Heng Li 2017-07-08 11:34:52 -04:00
parent cc554aee43
commit 1fee5f8edc
2 changed files with 9 additions and 5 deletions
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12
main.c
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@ -10,7 +10,7 @@
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r159-pre" #define MM_VERSION "2.0-r160-pre"
void liftrlimit() void liftrlimit()
{ {
@ -63,7 +63,7 @@ int main(int argc, char *argv[])
int minibatch_size = 200000000; int minibatch_size = 200000000;
uint64_t batch_size = 4000000000ULL; uint64_t batch_size = 4000000000ULL;
bseq_file_t *fp = 0; bseq_file_t *fp = 0;
char *fnw = 0; char *fnw = 0, *s;
FILE *fpr = 0, *fpw = 0; FILE *fpr = 0, *fpw = 0;
liftrlimit(); liftrlimit();
@ -93,8 +93,6 @@ int main(int argc, char *argv[])
else if (c == 'm') opt.min_chain_score = atoi(optarg); else if (c == 'm') opt.min_chain_score = atoi(optarg);
else if (c == 'A') opt.a = atoi(optarg); else if (c == 'A') opt.a = atoi(optarg);
else if (c == 'B') opt.b = atoi(optarg); else if (c == 'B') opt.b = atoi(optarg);
else if (c == 'O') opt.q = atoi(optarg);
else if (c == 'E') opt.e = atoi(optarg);
else if (c == 'z') opt.zdrop = atoi(optarg); else if (c == 'z') opt.zdrop = atoi(optarg);
else if (c == 's') opt.min_dp_max = atoi(optarg); else if (c == 's') opt.min_dp_max = atoi(optarg);
else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // --bucket-bits else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // --bucket-bits
@ -104,6 +102,12 @@ int main(int argc, char *argv[])
else if (c == 'V') { else if (c == 'V') {
puts(MM_VERSION); puts(MM_VERSION);
return 0; return 0;
} else if (c == 'O') {
opt.q = opt.q2 = strtol(optarg, &s, 10);
if (*s == ',') opt.q2 = strtol(s + 1, &s, 10);
} else if (c == 'E') {
opt.e = opt.e2 = strtol(optarg, &s, 10);
if (*s == ',') opt.e2 = strtol(s + 1, &s, 10);
} else if (c == 'I' || (c == 0 && long_idx == 1)) { } else if (c == 'I' || (c == 0 && long_idx == 1)) {
double x; double x;
char *p; char *p;

2
minimap2.1
View File

@ -1,4 +1,4 @@
.TH minimap2 1 "5 July 2017" "minimap2-2.0-r158-pre" "Bioinformatics tools" .TH minimap2 1 "8 July 2017" "minimap2-2.0-r160-pre" "Bioinformatics tools"
.SH NAME .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences minimap2 - mapping and alignment between collections of DNA sequences