diff --git a/CommandLines.cpp b/CommandLines.cpp index 6ae58c5..423baee 100644 --- a/CommandLines.cpp +++ b/CommandLines.cpp @@ -36,7 +36,7 @@ void Print_H(hifiasm_opt_t* asm_opt) fprintf(stderr, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round); 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, " -f INT number of bits for bloom filter; 0 to disable [%d]\n", asm_opt->bf_shift); fprintf(stderr, " -D FLOAT drop k-mers occuring >FLOAT*coverage times [%.1f]\n", asm_opt->high_factor); fprintf(stderr, " -N INT consider up to max(-D*coverage,-N) overlaps for each oriented read [%d]\n", asm_opt->max_n_chain); fprintf(stderr, " -i ignore saved overlaps in *.ovlp* files\n"); diff --git a/CommandLines.h b/CommandLines.h index bc2747c..b61d863 100644 --- a/CommandLines.h +++ b/CommandLines.h @@ -3,7 +3,7 @@ #include -#define HA_VERSION "0.3.0-dirty-r234" +#define HA_VERSION "0.3.0-dirty-r235" #define VERBOSE 0 diff --git a/hifiasm.1 b/hifiasm.1 index ce2ba07..0a5385e 100644 --- a/hifiasm.1 +++ b/hifiasm.1 @@ -91,11 +91,23 @@ Show version number. .SS Error correction options -.TP -.BI -k \ INT -K-mer length [40]. This option must be less than 64. - .TP 10 +.BI -k \ INT +K-mer length [51]. This option must be less than 64. + +.TP +.BI -w \ INT +Minimizer window size [51]. + +.TP +.BI -f \ INT +Number of bits for bloom filter; 0 to disable [37]. This bloom filter is used +to filter out singleton k-mers when counting all k-mers. It takes +.RI 2^( INT -3) +bytes of memory. A proper setting saves memory. 37 is recommended for human +assembly. + +.TP .BI -r \ INT Rounds of haplotype-aware error corrections [2]. This option affects all outputs of hifiasm.