diff --git a/fastmap.c b/fastmap.c index 8ffa07b..35797fd 100644 --- a/fastmap.c +++ b/fastmap.c @@ -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 diff --git a/main.c b/main.c index dd06b42..a177e6f 100644 --- a/main.c +++ b/main.c @@ -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[]);