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r764: changed -c in "-x pacbio" to 500

This commit is contained in:
Heng Li 2014-05-13 12:53:24 -04:00
parent a35a6c2580
commit 08517ac09b
2 changed files with 3 additions and 3 deletions
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4
fastmap.c
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@ -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;

2
main.c
View File

@ -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[]);