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Update for overlaps

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This commit is contained in:
Haoyu Cheng
2019-12-28 16:18:50 -05:00
parent 93ea81b2d2
commit ea248038c6
2 changed files with 6 additions and 4 deletions
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6
CommandLines.cpp
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@@ -29,6 +29,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -k INT k-mer length [%d] (must be < 64)\n", asm_opt->k_mer_length);
///fprintf(stderr, " -w write all overlaps to disk, can accelerate assembly next time [%d]\n", asm_opt->write_index_to_disk);
///fprintf(stderr, " -l load all overlaps from disk, can avoid overlap calculation [%d]\n", asm_opt->load_index_from_disk);
fprintf(stderr, " -i do the overlap calculation even if there are overlaps of previous run on disk.\n");
fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen);
fprintf(stderr, " -p INT size of popped bubbles [%lld]\n", asm_opt->pop_bubble_size);
fprintf(stderr, " -x FLOAT max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate);
@@ -199,7 +200,7 @@ 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:", 0)) >= 0) {
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:lwm:n:r:a:b:z:x:y:p:i", 0)) >= 0) {
if (c == 'h')
{
Print_H(asm_opt);
@@ -215,7 +216,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 'n') asm_opt->k_mer_min_freq = atoi(opt.arg);
else if (c == 'm') asm_opt->k_mer_max_freq = atoi(opt.arg);
else if (c == 'r') asm_opt->number_of_round = atoi(opt.arg);
else if (c == 'k') asm_opt->k_mer_length = atoi(opt.arg);
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 == 'a') asm_opt->clean_round = atoi(opt.arg);