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r218: increase the frequency of SW slightly

This commit is contained in:
Heng Li 2017-07-28 13:30:42 -04:00
parent f4fee60188
commit c672690564
2 changed files with 3 additions and 4 deletions
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5
align.c
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@ -160,8 +160,7 @@ static inline void mm_adjust_minier(const mm_idx_t *mi, uint8_t *const qseq0[2],
static void mm_filter_bad_seeds(void *km, int as1, int cnt1, mm128_t *a, int min_gap, int diff_thres, int max_ext_len, int max_ext_cnt)
{
int max_st, max_en, n, i, k, max;
int *K;
int max_st, max_en, n, i, k, max, *K;
for (i = 1, n = 0; i < cnt1; ++i) { // count the number of gaps longer than min_gap
int gap = ((int32_t)a[as1 + i].y - a[as1 + i - 1].y) - ((int32_t)a[as1 + i].x - a[as1 + i - 1].x);
if (gap < -min_gap || gap > min_gap) ++n;
@ -302,7 +301,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
if (a[as1+i].y & (MM_SEED_IGNORE|MM_SEED_TANDEM)) continue;
mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
re1 = re, qe1 = qe;
if (i == cnt1 - 1 || (a[as1+i].y&MM_SEED_LONG_JOIN) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
if (i == cnt1 - 1 || (a[as1+i].y&MM_SEED_LONG_JOIN) || (qe - qs >= opt->min_ksw_len && re - rs >= opt->min_ksw_len)) {
int bw1 = bw;
if (a[as1+i].y & MM_SEED_LONG_JOIN)
bw1 = qe - qs > re - rs? qe - qs : re - rs;

2
main.c
View File

@ -8,7 +8,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r217-dirty"
#define MM_VERSION "2.0-r218-dirty"
void liftrlimit()
{