diff --git a/bwamem.c b/bwamem.c index d29fcae..0f400b0 100644 --- a/bwamem.c +++ b/bwamem.c @@ -376,7 +376,7 @@ int mem_patch_reg(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, if (bwa_verbose >= 4) printf("* potential hit merge between [%d,%d)<=>[%ld,%ld) and [%d,%d)<=>[%ld,%ld), @ %s; w=%d, r=%.4g\n", a->qb, a->qe, (long)a->rb, (long)a->re, b->qb, b->qe, (long)b->rb, (long)b->re, bns->anns[a->rid].name, w, r); - if (w > opt->w) return 0; // the bandwidth is too large + if (w > opt->w<<1) return 0; // the bandwidth is too large if (r >= PATCH_MAX_R_BW) return 0; // relative bandwidth is too large // global alignment w += a->w + b->w; diff --git a/fastmap.c b/fastmap.c index 2810a36..655272d 100644 --- a/fastmap.c +++ b/fastmap.c @@ -147,8 +147,8 @@ 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", 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 -B5 -O2 -E1 -L0\n"); - fprintf(stderr, " pbread: -k13 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -N25 -FeaD.001\n"); + fprintf(stderr, " pacbio: -k17 -W40 -c1000 -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"); fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n"); @@ -178,7 +178,6 @@ 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.w) opt->w = 200; 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; diff --git a/main.c b/main.c index 23d067d..edc129c 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.8-r728-dirty" +#define PACKAGE_VERSION "0.7.8-r729-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);