xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-15 12:47:57 +08:00
Code Issues Packages Projects Releases Wiki Activity

improve speed

Browse Source
This commit is contained in:
Haoyu Cheng
2019-08-26 02:22:20 -04:00
parent 6802d873cf
commit 3c0c201cdf
12 changed files with 249 additions and 39 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
CommandLines.cpp
View File

@@ -10,8 +10,8 @@ char* output_file_name = NULL;
int thread_num = 1;
int k_mer_length = 40;
//int k_mer_min_freq = 9;
//int k_mer_min_freq = 3;
int k_mer_min_freq = 2;
int k_mer_min_freq = 3;
//int k_mer_min_freq = 2;
int k_mer_max_freq = 66;
int load_index_from_disk = 0;
int write_index_to_disk = 0;
@@ -36,21 +36,25 @@ int CommandLine_process (int argc, char *argv[])
{
static ko_longopt_t longopts[] = {
{ "help", ko_no_argument, 100},
{ "help", ko_no_argument, 100},
{ "seq", ko_required_argument, 101},
{ "output", ko_required_argument, 102},
{ "thread", ko_required_argument, 103},
{ "k_mer_min_freq", ko_required_argument, 104},
{ "k_mer_max_freq", ko_required_argument, 105},
{ NULL, 0, 0 }
};
ketopt_t opt = KETOPT_INIT;
int i, c;
while ((c = ketopt(&opt, argc, argv, 1, "ht:o:q:k:lw", longopts)) >= 0) {
while ((c = ketopt(&opt, argc, argv, 1, "ht:o:q:k:lwm:n:", longopts)) >= 0) {
if (c == 100 || c == 'h') Print_H();
else if (c == 103 || c == 't') thread_num = atoi(opt.arg);
else if (c == 102 || c == 'o') output_file_name = opt.arg;
else if (c == 101 || c == 'q') read_file_name = opt.arg;
else if (c == 104 || c == 'n') k_mer_min_freq = atoi(opt.arg);
else if (c == 105 || c == 'm') k_mer_max_freq = atoi(opt.arg);
else if (c == 'k') k_mer_length = atoi(opt.arg);
else if (c == 'l') load_index_from_disk = 1;
else if (c == 'w') write_index_to_disk = 1;