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NOT WORKING!!! added all k-mer counter

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Heng Li
2020-03-24 12:29:46 -04:00
parent 398e73022b
commit 64edb06e08
15 changed files with 628 additions and 237 deletions
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CommandLines.cpp
+6 -3
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@@ -28,6 +28,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
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, " -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, " -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");
@@ -63,7 +64,8 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->pat_index = NULL;
asm_opt->mat_index = NULL;
asm_opt->thread_num = 1;
asm_opt->k_mer_length = 39;
asm_opt->k_mer_length = 41;
asm_opt->bf_shift = 37;
asm_opt->k_mer_min_freq = 3;
asm_opt->k_mer_max_freq = 66;
asm_opt->load_index_from_disk = 1;
@@ -295,7 +297,7 @@ 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:i", 0)) >= 0) {
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) {
if (c == 'h')
{
Print_H(asm_opt);
@@ -305,7 +307,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
{
fprintf(stderr, "[Version] %s\n", VERSION);
return 0;
}
}
else if (c == 'f') asm_opt->bf_shift = atoi(opt.arg);
else if (c == 't') asm_opt->thread_num = atoi(opt.arg);
else if (c == 'o') asm_opt->output_file_name = opt.arg;
else if (c == 'r') asm_opt->number_of_round = atoi(opt.arg);