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dev-464: preset for pacbio read2read aln

This commit is contained in:
Heng Li 2014-04-08 11:40:54 -04:00
parent 172ba83241
commit b45aeb87e1
2 changed files with 14 additions and 7 deletions
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19
fastmap.c
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@ -145,6 +145,7 @@ 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 -w200 -c1000 -r10 -A2 -B5 -O2 -E1\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");
@ -166,21 +167,27 @@ int main_mem(int argc, char *argv[])
}
if (mode) {
if (strcmp(mode, "pacbio") == 0) {
if (strcmp(mode, "pacbio") == 0 || strcmp(mode, "pbref") == 0 || strcmp(mode, "pbread") == 0) {
if (!opt0.a) opt->a = 2, opt0.a = 1;
update_a(opt, &opt0);
if (!opt0.b) opt->b = 7;
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.w) opt->w = 200;
if (!opt0.min_seed_len) opt->min_seed_len = 17;
if (!opt0.min_chain_weight) opt->min_chain_weight = 40;
if (!opt0.max_occ) opt->max_occ = 1000;
if (!opt0.pen_clip5) opt->pen_clip5 = 0;
if (!opt0.pen_clip3) opt->pen_clip3 = 0;
if (opt0.split_factor == 0.) opt->split_factor = 10.;
if (strcmp(mode, "pbread") == 0) {
if (!opt0.b) opt->b = 5;
if (!opt0.min_seed_len) opt->min_seed_len = 13;
if (!opt0.min_chain_weight) opt->min_chain_weight = 30;
} else {
if (!opt0.b) opt->b = 7;
if (!opt0.min_seed_len) opt->min_seed_len = 17;
if (!opt0.min_chain_weight) opt->min_chain_weight = 40;
if (!opt0.pen_clip5) opt->pen_clip5 = 0;
if (!opt0.pen_clip3) opt->pen_clip3 = 0;
}
} else {
fprintf(stderr, "[E::%s] unknown read type '%s'\n", __func__, mode);
return 1; // FIXME memory leak

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8+dev-r463"
#define PACKAGE_VERSION "0.7.8+dev-r464"
#endif
int bwa_fa2pac(int argc, char *argv[]);