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r760: removed commented code 

It is slow and is not very effective. And I hate useless code.
This commit is contained in:
Heng Li 2014-05-09 14:59:07 -04:00
parent 43b498a37e
commit cfe6996173
2 changed files with 1 additions and 20 deletions
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19
bwamem.c
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@ -133,25 +133,6 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, int len, co
for (i = 0; i < a->mem1.n; ++i) for (i = 0; i < a->mem1.n; ++i)
if ((a->mem1.a[i].info>>32) - (uint32_t)a->mem1.a[i].info >= opt->min_seed_len) if ((a->mem1.a[i].info>>32) - (uint32_t)a->mem1.a[i].info >= opt->min_seed_len)
kv_push(bwtintv_t, a->mem, a->mem1.a[i]); kv_push(bwtintv_t, a->mem, a->mem1.a[i]);
/*
{ // third pass:
int max_len = 0, max_i = -1;
for (i = 0; i < a->mem1.n; ++i) {
bwtintv_t *q = &a->mem1.a[i];
int start = q->info>>32, end = (int32_t)q->info;
if (end - start > max_len)
max_len = end - start, max_i = i;
}
if (max_i >= 0 && max_len > .9 * (end - start) && max_len >= split_len) {
bwtintv_t t = a->mem1.a[max_i];
int start = t.info>>32, end = (int32_t)t.info;
bwt_smem1(bwt, len, seq, (start + end)>>1, t.x[2]+1, &a->mem1, a->tmpv);
for (i = 0; i < a->mem1.n; ++i)
if ((a->mem1.a[i].info>>32) - (uint32_t)a->mem1.a[i].info >= opt->min_seed_len)
kv_push(bwtintv_t, a->mem, a->mem1.a[i]);
}
}
*/
} }
// sort // sort
ks_introsort(mem_intv, a->mem.n, a->mem.a); ks_introsort(mem_intv, a->mem.n, a->mem.a);

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8-r759-dirty" #define PACKAGE_VERSION "0.7.8-r760-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);