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S/L index&reads

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This commit is contained in:
Haoyu Cheng
2019-05-16 21:14:50 -04:00
parent 3c5799aa1b
commit 17553e0a42
14 changed files with 297 additions and 5 deletions
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CommandLines.cpp
+6 -1
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@@ -11,6 +11,9 @@ int thread_num = 1;
int k_mer_length = 40;
int k_mer_min_freq = 9;
int k_mer_max_freq = 66;
int load_index_from_disk = 0;
int write_index_to_disk = 0;
double Get_T(void)
{
@@ -41,12 +44,14 @@ int CommandLine_process (int argc, char *argv[])
ketopt_t opt = KETOPT_INIT;
int i, c;
while ((c = ketopt(&opt, argc, argv, 1, "ht:o:q:k:", longopts)) >= 0) {
while ((c = ketopt(&opt, argc, argv, 1, "ht:o:q:k:lw", 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 == '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;
else if (c == '?') printf("unknown opt: -%c\n", opt.opt? opt.opt : ':');
else if (c == ':') printf("missing arg: -%c\n", opt.opt? opt.opt : ':');
}