From a6b5a30dabb254aa6534c4ec80d531413d22e12d Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 20 Oct 2014 17:34:15 -0400 Subject: [PATCH] r930: use 3rd round seeding by default This strategy is similar to the seeding heuristic used by LAST. When it is used alone, it is not as accurate as the current seeding strategy at least for short reads. However, it may do a better job for a long contig mapped to multiple ALT contigs. This seeding strategy is also relatively cheap to perform. --- bwamem.c | 2 +- fastmap.c | 2 +- main.c | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/bwamem.c b/bwamem.c index 95478a6..71bf387 100644 --- a/bwamem.c +++ b/bwamem.c @@ -59,7 +59,7 @@ mem_opt_t *mem_opt_init() o->pen_unpaired = 17; o->pen_clip5 = o->pen_clip3 = 5; - o->max_mem_intv = 0; + o->max_mem_intv = 10; o->min_seed_len = 19; o->split_width = 10; diff --git a/fastmap.c b/fastmap.c index e949da3..ddf464a 100644 --- a/fastmap.c +++ b/fastmap.c @@ -145,7 +145,7 @@ int main_mem(int argc, char *argv[]) fprintf(stderr, " -w INT band width for banded alignment [%d]\n", opt->w); fprintf(stderr, " -d INT off-diagonal X-dropoff [%d]\n", opt->zdrop); fprintf(stderr, " -r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor); - fprintf(stderr, " -y INT find MEMs longer than {-k} * {-r} with size less than INT (EXPERIMENTAL) [%ld]\n", (long)opt->max_mem_intv); + fprintf(stderr, " -y INT seed occurrence for the 3rd round seeding [%ld]\n", (long)opt->max_mem_intv); // fprintf(stderr, " -s INT look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width); fprintf(stderr, " -c INT skip seeds with more than INT occurrences [%d]\n", opt->max_occ); fprintf(stderr, " -D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping chain [%.2f]\n", opt->drop_ratio); diff --git a/main.c b/main.c index 54f93fe..e8fb688 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.10-r929-dirty" +#define PACKAGE_VERSION "0.7.10-r930-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);