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r1163: increased the default -I to 8G 

To reduce accidental errors when mapping against diploid human assemblies.
This commit is contained in:
Heng Li 2023-04-07 01:22:22 -04:00
parent ea2042a577
commit a026c69b89
4 changed files with 4 additions and 4 deletions
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2
main.c
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@ -325,7 +325,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -k INT k-mer size (no larger than 28) [%d]\n", ipt.k); fprintf(fp_help, " -k INT k-mer size (no larger than 28) [%d]\n", ipt.k);
fprintf(fp_help, " -w INT minimizer window size [%d]\n", ipt.w); fprintf(fp_help, " -w INT minimizer window size [%d]\n", ipt.w);
// fprintf(fp_help, " -j INT syncmer submer size (overriding -w) []\n"); // fprintf(fp_help, " -j INT syncmer submer size (overriding -w) []\n");
fprintf(fp_help, " -I NUM split index for every ~NUM input bases [4G]\n"); fprintf(fp_help, " -I NUM split index for every ~NUM input bases [8G]\n");
fprintf(fp_help, " -d FILE dump index to FILE []\n"); fprintf(fp_help, " -d FILE dump index to FILE []\n");
fprintf(fp_help, " Mapping:\n"); fprintf(fp_help, " Mapping:\n");
fprintf(fp_help, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%g]\n", opt.mid_occ_frac); fprintf(fp_help, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%g]\n", opt.mid_occ_frac);

2
minimap.h
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@ -5,7 +5,7 @@
#include <stdio.h> #include <stdio.h>
#include <sys/types.h> #include <sys/types.h>
#define MM_VERSION "2.24-r1162-dirty" #define MM_VERSION "2.24-r1163-dirty"
#define MM_F_NO_DIAG 0x001 // no exact diagonal hit #define MM_F_NO_DIAG 0x001 // no exact diagonal hit
#define MM_F_NO_DUAL 0x002 // skip pairs where query name is lexicographically larger than target name #define MM_F_NO_DUAL 0x002 // skip pairs where query name is lexicographically larger than target name

2
minimap2.1
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@ -101,7 +101,7 @@ on the HPC sequence.
.BI -I \ NUM .BI -I \ NUM
Load at most Load at most
.I NUM .I NUM
target bases into RAM for indexing [4G]. If there are more than target bases into RAM for indexing [8G]. If there are more than
.I NUM .I NUM
bases in bases in
.IR target.fa , .IR target.fa ,

2
options.c
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@ -8,7 +8,7 @@ void mm_idxopt_init(mm_idxopt_t *opt)
opt->k = 15, opt->w = 10, opt->flag = 0; opt->k = 15, opt->w = 10, opt->flag = 0;
opt->bucket_bits = 14; opt->bucket_bits = 14;
opt->mini_batch_size = 50000000; opt->mini_batch_size = 50000000;
opt->batch_size = 4000000000ULL; opt->batch_size = 8000000000ULL;
} }
void mm_mapopt_init(mm_mapopt_t *opt) void mm_mapopt_init(mm_mapopt_t *opt)