From c6726905644a57587625080d3c60111dfc7216aa Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 28 Jul 2017 13:30:42 -0400 Subject: [PATCH] r218: increase the frequency of SW slightly --- align.c | 5 ++--- main.c | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/align.c b/align.c index 192c6c7..93c8371 100644 --- a/align.c +++ b/align.c @@ -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; diff --git a/main.c b/main.c index fc67289..0c59795 100644 --- a/main.c +++ b/main.c @@ -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() {