zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

dev-469: fixed wrong command line prompt

This commit is contained in:
Heng Li 2014-04-09 13:20:04 -04:00
parent d766591c1e
commit db58392e9b
2 changed files with 4 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
fastmap.c
View File

@ -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, " -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, " -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, " 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, "\nInput/output options:\n\n");
fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\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"); 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 (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; if (!opt0.a) opt->a = 2, opt0.a = 1;
update_a(opt, &opt0); update_a(opt, &opt0);
if (!opt0.o_del) opt->o_del = 2; 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.e_ins) opt->e_ins = 1;
if (!opt0.max_occ) opt->max_occ = 1000; if (!opt0.max_occ) opt->max_occ = 1000;
if (opt0.split_factor == 0.) opt->split_factor = 10.; 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; opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG;
if (!opt0.b) opt->b = 5; if (!opt0.b) opt->b = 5;
if (!opt0.w) opt->w = 100; if (!opt0.w) opt->w = 100;

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8+dev-r468" #define PACKAGE_VERSION "0.7.8+dev-r469"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);