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r828: changed the default scoring for pacbio

This commit is contained in:
Heng Li 2014-09-15 23:22:05 -04:00
parent b07587f806
commit 5d26ab0ee3
2 changed files with 7 additions and 7 deletions
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12
fastmap.c
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@ -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) {

2
main.c
View File

@ -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[]);