From db58392e9baa7606a6c9d6b48ba4e26f0b89cc7a Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 9 Apr 2014 13:20:04 -0400 Subject: [PATCH] dev-469: fixed wrong command line prompt --- fastmap.c | 6 +++--- main.c | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/fastmap.c b/fastmap.c index f3dd2f6..9bdacb4 100644 --- a/fastmap.c +++ b/fastmap.c @@ -147,7 +147,7 @@ int main_mem(int argc, char *argv[]) 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 -w200 -c1000 -r10 -A2 -B7 -O2 -E1 -L0\n"); - fprintf(stderr, " pbread: -k13 -W30 -w100 -c1000 -r10 -A2 -B5 -O2 -E1 -aeD.02\n"); + fprintf(stderr, " pbread: -k13 -W30 -w100 -c1000 -r10 -A2 -B5 -O2 -E1 -N20 -FeaD.01\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"); @@ -169,7 +169,7 @@ int main_mem(int argc, char *argv[]) } if (mode) { - if (strcmp(mode, "pacbio") == 0 || strcmp(mode, "pbref") == 0 || strcmp(mode, "pbread1") == 0) { + 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; update_a(opt, &opt0); if (!opt0.o_del) opt->o_del = 2; @@ -178,7 +178,7 @@ int main_mem(int argc, char *argv[]) if (!opt0.e_ins) opt->e_ins = 1; if (!opt0.max_occ) opt->max_occ = 1000; if (opt0.split_factor == 0.) opt->split_factor = 10.; - if (strcmp(mode, "pbread1") == 0) { + if (strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) { opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG; if (!opt0.b) opt->b = 5; if (!opt0.w) opt->w = 100; diff --git a/main.c b/main.c index b100b8d..91f28bc 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.8+dev-r468" +#define PACKAGE_VERSION "0.7.8+dev-r469" #endif int bwa_fa2pac(int argc, char *argv[]);