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r235: clarified option -f

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Heng Li
2020-04-12 19:42:02 -04:00
parent cdd5f3e4e0
commit cc166c8ff5
3 changed files with 18 additions and 6 deletions
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CommandLines.cpp
+1 -1
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@@ -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, " -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, " -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, " -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, " -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, " -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"); fprintf(stderr, " -i ignore saved overlaps in *.ovlp* files\n");
CommandLines.h
+1 -1
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@@ -3,7 +3,7 @@
#include <pthread.h> #include <pthread.h>
#define HA_VERSION "0.3.0-dirty-r234" #define HA_VERSION "0.3.0-dirty-r235"
#define VERBOSE 0 #define VERBOSE 0
hifiasm.1
+16 -4
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@@ -91,11 +91,23 @@ Show version number.
.SS Error correction options .SS Error correction options
.TP
.BI -k \ INT
K-mer length [40]. This option must be less than 64.
.TP 10 .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 .BI -r \ INT
Rounds of haplotype-aware error corrections [2]. This option affects all outputs of hifiasm. Rounds of haplotype-aware error corrections [2]. This option affects all outputs of hifiasm.