From 5d26ab0ee3e4b4e19f5ccc7a3a9ecc455075f110 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 15 Sep 2014 23:22:05 -0400 Subject: [PATCH] r828: changed the default scoring for pacbio --- fastmap.c | 12 ++++++------ main.c | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/fastmap.c b/fastmap.c index c141383..05a5954 100644 --- a/fastmap.c +++ b/fastmap.c @@ -153,8 +153,8 @@ 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\n", opt->pen_unpaired); fprintf(stderr, " -x STR read type. Setting -x changes multiple parameters unless overriden [null]\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, " pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0\n"); +// fprintf(stderr, " pbread: -k13 -W40 -c1000 -r10 -A1 -B1 -O1 -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"); fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n"); @@ -180,13 +180,13 @@ int main_mem(int argc, char *argv[]) if (mode) { if (strcmp(mode, "pacbio") == 0 || strcmp(mode, "pbref") == 0 || strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) { - if (!opt0.a) opt->a = 2, opt0.a = 1; + if (!opt0.a) opt->a = 1, opt0.a = 1; update_a(opt, &opt0); - if (!opt0.o_del) opt->o_del = 2; + if (!opt0.o_del) opt->o_del = 1; if (!opt0.e_del) opt->e_del = 1; - if (!opt0.o_ins) opt->o_ins = 2; + if (!opt0.o_ins) opt->o_ins = 1; if (!opt0.e_ins) opt->e_ins = 1; - if (!opt0.b) opt->b = 5; + if (!opt0.b) opt->b = 1; 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) { diff --git a/main.c b/main.c index 8c34b1b..3edac05 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.10-r827-dirty" +#define PACKAGE_VERSION "0.7.10-r828-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);