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phasing

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This commit is contained in:
Haoyu Cheng
2019-09-02 10:30:14 -04:00
parent 3c0c201cdf
commit d5327fe9ee
15 changed files with 3396 additions and 656 deletions
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CommandLines.cpp
+4 -1
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@@ -15,6 +15,7 @@ int k_mer_min_freq = 3;
int k_mer_max_freq = 66;
int load_index_from_disk = 0;
int write_index_to_disk = 0;
int number_of_round = 1;
double Get_T(void)
@@ -42,19 +43,21 @@ int CommandLine_process (int argc, char *argv[])
{ "thread", ko_required_argument, 103},
{ "k_mer_min_freq", ko_required_argument, 104},
{ "k_mer_max_freq", ko_required_argument, 105},
{ "round", ko_required_argument, 106},
{ NULL, 0, 0 }
};
ketopt_t opt = KETOPT_INIT;
int i, c;
while ((c = ketopt(&opt, argc, argv, 1, "ht:o:q:k:lwm:n:", longopts)) >= 0) {
while ((c = ketopt(&opt, argc, argv, 1, "ht:o:q:k:lwm:n:r:", 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 == 106 || c == 'r') number_of_round = 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;