From 08517ac09bbd846cc1e6328ee66380f59cad3719 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 13 May 2014 12:53:24 -0400 Subject: [PATCH] r764: changed -c in "-x pacbio" to 500 --- fastmap.c | 4 ++-- main.c | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/fastmap.c b/fastmap.c index c8b2eb0..479e878 100644 --- a/fastmap.c +++ b/fastmap.c @@ -148,7 +148,7 @@ int main_mem(int argc, char *argv[]) fprintf(stderr, " -L INT[,INT] penalty for 5'- and 3'-end clipping [%d,%d]\n", opt->pen_clip5, opt->pen_clip3); fprintf(stderr, " -U INT penalty for an unpaired read pair [%d]\n", opt->pen_unpaired); fprintf(stderr, " -x STR read type. Setting -x changes multiple parameters unless overriden [null]\n"); - fprintf(stderr, " pacbio: -k17 -W40 -c1000 -r10 -A2 -B5 -O2 -E1 -L0\n"); + fprintf(stderr, " pacbio: -k17 -W40 -r10 -A2 -B5 -O2 -E1 -L0\n"); fprintf(stderr, " pbread: -k13 -W40 -c1000 -r10 -A2 -B5 -O2 -E1 -N25 -FeaD.001\n"); fprintf(stderr, "\nInput/output options:\n\n"); fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\n"); @@ -181,11 +181,11 @@ int main_mem(int argc, char *argv[]) if (!opt0.o_ins) opt->o_ins = 2; if (!opt0.e_ins) opt->e_ins = 1; if (!opt0.b) opt->b = 5; - if (!opt0.max_occ) opt->max_occ = 1000; if (opt0.split_factor == 0.) opt->split_factor = 10.; if (!opt0.min_chain_weight) opt->min_chain_weight = 40; if (strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) { opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG; + if (!opt0.max_occ) opt->max_occ = 1000; if (!opt0.min_seed_len) opt->min_seed_len = 13; if (!opt0.max_chain_extend) opt->max_chain_extend = 25; if (opt0.drop_ratio == 0.) opt->drop_ratio = .001; diff --git a/main.c b/main.c index e006542..51c446c 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.8-r762-dirty" +#define PACKAGE_VERSION "0.7.8-r764-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);