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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.
This commit is contained in:
Heng Li 2014-10-20 17:34:15 -04:00
parent 038af2a551
commit a6b5a30dab
3 changed files with 3 additions and 3 deletions
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2
bwamem.c
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@ -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;

2
fastmap.c
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@ -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);

2
main.c
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@ -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[]);