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r768: shortened preset; added dv tag (#25) 

Also added asm20 to command line help (#151)
This commit is contained in:
Heng Li 2018-04-24 12:48:54 -04:00
parent 39f836eac8
commit aef7b0744c
2 changed files with 9 additions and 11 deletions
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19
main.c
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@ -10,7 +10,7 @@
#include "getopt.h"
#endif
#define MM_VERSION "2.10-r764-dirty"
#define MM_VERSION "2.10-r768-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -243,7 +243,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, "Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]\n");
fprintf(fp_help, "Options:\n");
fprintf(fp_help, " Indexing:\n");
fprintf(fp_help, " -H use homopolymer-compressed k-mer\n");
fprintf(fp_help, " -H use homopolymer-compressed k-mer (preferrable for PacBio)\n");
fprintf(fp_help, " -k INT k-mer size (no larger than 28) [%d]\n", ipt.k);
fprintf(fp_help, " -w INT minizer window size [%d]\n", ipt.w);
fprintf(fp_help, " -I NUM split index for every ~NUM input bases [4G]\n");
@ -282,15 +282,12 @@ int main(int argc, char *argv[])
// fprintf(fp_help, " -v INT verbose level [%d]\n", mm_verbose);
fprintf(fp_help, " --version show version number\n");
fprintf(fp_help, " Preset:\n");
fprintf(fp_help, " -x STR preset (always applied before other options) []\n");
fprintf(fp_help, " map-pb: -Hk19 (PacBio vs reference mapping)\n");
fprintf(fp_help, " map-ont: -k15 (Oxford Nanopore vs reference mapping)\n");
fprintf(fp_help, " asm5: -k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5%% div.)\n");
fprintf(fp_help, " asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10%% div.)\n");
fprintf(fp_help, " ava-pb: -Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25 (PacBio read overlap)\n");
fprintf(fp_help, " ava-ont: -k15 -Xw5 -m100 -g10000 -r2000 --max-chain-skip 25 (ONT read overlap)\n");
fprintf(fp_help, " splice: long-read spliced alignment (see minimap2.1 for details)\n");
fprintf(fp_help, " sr: short single-end reads without splicing (see minimap2.1 for details)\n");
fprintf(fp_help, " -x STR preset (always applied before other options; see minimap2.1 for details) []\n");
fprintf(fp_help, " - map-pb/map-ont: PacBio/Nanopore vs reference mapping\n");
fprintf(fp_help, " - ava-pb/ava-ont: PacBio/Nanopore read overlap\n");
fprintf(fp_help, " - asm5/asm10/asm20: asm-to-ref mapping, for ~0.1/1/5%% sequence divergence\n");
fprintf(fp_help, " - splice: long-read spliced alignment\n");
fprintf(fp_help, " - sr: genomic short-read mapping\n");
fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n");
return fp_help == stdout? 0 : 1;
}

1
minimap2.1
View File

@ -572,6 +572,7 @@ nn i Number of ambiguous bases in the alignment
ts A Transcript strand (splice mode only)
cg Z CIGAR string (only in PAF)
cs Z Difference string
dv f Approximate per-base sequence divergence
.TE
.PP