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option to skip k-mer filtering

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This commit is contained in:
Heng Li
2020-03-27 22:32:39 -04:00
parent 19648873b9
commit 5e16483b43
4 changed files with 29 additions and 9 deletions
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CommandLines.cpp
+4 -2
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@@ -29,7 +29,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
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, " -D FLOAT drop k-mers occuring more than FLOAT*coverage times [%.1f]\n", asm_opt->high_factor);
fprintf(stderr, " -D FLOAT drop k-mers occuring >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");
@@ -69,6 +69,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->bf_shift = 37;
asm_opt->high_factor = 7.0f;
asm_opt->no_HPC = 0;
asm_opt->no_kmer_flt = 0;
asm_opt->k_mer_min_freq = 3;
asm_opt->k_mer_max_freq = 66;
asm_opt->load_index_from_disk = 1;
@@ -300,7 +301,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
int c;
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:lw:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:", 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:F", 0)) >= 0) {
if (c == 'h')
{
Print_H(asm_opt);
@@ -320,6 +321,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 'l') asm_opt->load_index_from_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 == 'F') asm_opt->no_kmer_flt = 1;
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;