From 5ef9580b17c3573dbd23ea9dfbf9cdfbcc7d6b30 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 23 Mar 2018 10:15:23 -0400 Subject: [PATCH] r753: change bandwidth in ava-ont to 2000bp --- main.c | 4 ++-- minimap2.1 | 2 +- options.c | 1 + 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/main.c b/main.c index a23866a..315b8c7 100644 --- a/main.c +++ b/main.c @@ -10,7 +10,7 @@ #include "getopt.h" #endif -#define MM_VERSION "2.9-r752-dirty" +#define MM_VERSION "2.9-r753-dirty" #ifdef __linux__ #include @@ -286,7 +286,7 @@ int main(int argc, char *argv[]) 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 --max-chain-skip 25 (ONT 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, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n"); diff --git a/minimap2.1 b/minimap2.1 index 0305b41..6011634 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -484,7 +484,7 @@ PacBio all-vs-all overlap mapping .B ava-ont Oxford Nanopore all-vs-all overlap mapping .RB ( -k15 -.B -Xw5 -m100 -g10000 --max-chain-skip +.B -Xw5 -m100 -g10000 -r2000 --max-chain-skip .BR 25 ). Similarly, the major difference from .B ava-pb diff --git a/options.c b/options.c index e820484..04807c5 100644 --- a/options.c +++ b/options.c @@ -76,6 +76,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo) io->flag |= MM_I_HPC, io->k = 19, io->w = 5; mo->flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN; mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_gap = 10000, mo->max_chain_skip = 25; + mo->bw = 2000; } else if (strcmp(preset, "map10k") == 0 || strcmp(preset, "map-pb") == 0) { io->flag |= MM_I_HPC, io->k = 19; } else if (strcmp(preset, "map-ont") == 0) {