From aef7b0744cf236852f027538adb281b5275ed678 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 24 Apr 2018 12:48:54 -0400 Subject: [PATCH] r768: shortened preset; added dv tag (#25) Also added asm20 to command line help (#151) --- main.c | 19 ++++++++----------- minimap2.1 | 1 + 2 files changed, 9 insertions(+), 11 deletions(-) diff --git a/main.c b/main.c index 7fba060..4dc7205 100644 --- a/main.c +++ b/main.c @@ -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 @@ -243,7 +243,7 @@ int main(int argc, char *argv[]) fprintf(fp_help, "Usage: minimap2 [options] | [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; } diff --git a/minimap2.1 b/minimap2.1 index 4214708..0208ea9 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -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