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exposed mz_win and high_factor to CLI

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Heng Li
2020-03-27 21:39:57 -04:00
parent cb20e50219
commit 19648873b9
1 changed files with 6 additions and 5 deletions
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CommandLines.cpp
+6 -5
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@@ -23,13 +23,13 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, "Options:\n");
fprintf(stderr, " Assembly:\n");
fprintf(stderr, " -o FILE prefix of output files [%s]\n", asm_opt->output_file_name);
///fprintf(stderr, " -c FILE file including trio information\n");
fprintf(stderr, " -t INT number of threads [%d]\n", asm_opt->thread_num);
fprintf(stderr, " -r INT round of correction [%d]\n", asm_opt->number_of_round);
fprintf(stderr, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round);
fprintf(stderr, " -k INT k-mer length [%d] (must be < 64)\n", asm_opt->k_mer_length);
fprintf(stderr, " -k INT k-mer length (must be <64) [%d]\n", asm_opt->k_mer_length);
fprintf(stderr, " -w INT minimizer window size [%d]\n", asm_opt->mz_win);
fprintf(stderr, " -f INT number of bits for bloom filter [%d]\n", asm_opt->bf_shift);
///fprintf(stderr, " -w write all overlaps to disk, can accelerate assembly next time [%d]\n", asm_opt->write_index_to_disk);
fprintf(stderr, " -D FLOAT drop k-mers occuring more than FLOAT*coverage times [%.1f]\n", asm_opt->high_factor);
///fprintf(stderr, " -l load all overlaps from disk, can avoid overlap calculation [%d]\n", asm_opt->load_index_from_disk);
///fprintf(stderr, " -i ignore saved overlaps in *.ovlp*.bin files\n");
fprintf(stderr, " -i ignore saved overlaps in *.ovlp* files\n");
@@ -300,7 +300,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
int c;
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:lwm:n:r:a:b:z:x:y:p:c:d:M:P:if:", 0)) >= 0) {
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:lw:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:", 0)) >= 0) {
if (c == 'h')
{
Print_H(asm_opt);
@@ -318,7 +318,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 'k') asm_opt->k_mer_length = atoi(opt.arg);
else if (c == 'i') asm_opt->load_index_from_disk = 0;
else if (c == 'l') asm_opt->load_index_from_disk = 1;
else if (c == 'w') asm_opt->write_index_to_disk = 1;
else if (c == 'w') asm_opt->mz_win = atoi(opt.arg);
else if (c == 'D') asm_opt->high_factor = atof(opt.arg);
else if (c == 'a') asm_opt->clean_round = atoi(opt.arg);
else if (c == 'z') asm_opt->adapterLen = atoi(opt.arg);
else if (c == 'b') asm_opt->required_read_name = opt.arg;