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r707: change params for pacbio-to-pacbio

This commit is contained in:
Heng Li 2014-04-10 21:53:52 -04:00
parent 658f27eae4
commit bbcabfe342
2 changed files with 15 additions and 9 deletions
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22
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 -N20 -FeaD.01\n"); fprintf(stderr, " pbread: -k13 -W30 -w100 -c1000 -r10 -A1 -B1 -O0 -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");
@ -170,23 +170,29 @@ int main_mem(int argc, char *argv[])
if (mode) { if (mode) {
if (strcmp(mode, "pacbio") == 0 || strcmp(mode, "pbref") == 0 || strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 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;
if (!opt0.e_del) opt->e_del = 1;
if (!opt0.o_ins) opt->o_ins = 2;
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 || strcmp(mode, "pbread") == 0) { if (strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) {
if (!opt0.a) opt->a = 1, opt0.a = 1;
update_a(opt, &opt0);
if (!opt0.o_del) opt->o_del = 0;
if (!opt0.e_del) opt->e_del = 1;
if (!opt0.o_ins) opt->o_ins = 0;
if (!opt0.e_ins) opt->e_ins = 1;
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 = 1;
if (!opt0.w) opt->w = 100; if (!opt0.w) opt->w = 100;
if (!opt0.min_seed_len) opt->min_seed_len = 13; if (!opt0.min_seed_len) opt->min_seed_len = 13;
if (!opt0.min_chain_weight) opt->min_chain_weight = 30; if (!opt0.min_chain_weight) opt->min_chain_weight = 30;
if (!opt0.max_chain_extend) opt->max_chain_extend = 20; if (!opt0.max_chain_extend) opt->max_chain_extend = 20;
if (opt0.drop_ratio == 0.) opt->drop_ratio = .01; if (opt0.drop_ratio == 0.) opt->drop_ratio = .01;
} else { } else {
if (!opt0.a) opt->a = 2, opt0.a = 1;
update_a(opt, &opt0);
if (!opt0.o_del) opt->o_del = 2;
if (!opt0.e_del) opt->e_del = 1;
if (!opt0.o_ins) opt->o_ins = 2;
if (!opt0.e_ins) opt->e_ins = 1;
if (!opt0.b) opt->b = 7; if (!opt0.b) opt->b = 7;
if (!opt0.w) opt->w = 200; if (!opt0.w) opt->w = 200;
if (!opt0.min_seed_len) opt->min_seed_len = 17; if (!opt0.min_seed_len) opt->min_seed_len = 17;

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-r705-dirty" #define PACKAGE_VERSION "0.7.8-r707-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);