From 6088dc11ffb3db15c0057b80ca07cdb5cfa4d412 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 23 Jun 2017 23:24:49 -0400 Subject: [PATCH] wrong SW score --- align.c | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/align.c b/align.c index 30fb02a..10f6fdf 100644 --- a/align.c +++ b/align.c @@ -132,7 +132,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int ksw_extz2_sse(km, ql, qseq, tl, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_EXTZ_ONLY|KSW_EZ_RIGHT|KSW_EZ_REV_CIGAR, ez); mm_append_cigar(r, ez->n_cigar, ez->cigar); mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar); - r->p->score += ez->score; + r->p->score += ez->max; rs1 = rs - (ez->max_t + 1); qs1 = qs - (ez->max_q + 1); mm_seq_rev(ql, qseq); @@ -170,7 +170,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int ksw_extz2_sse(km, qe0-qe, qseq, re0-re, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_EXTZ_ONLY, ez); mm_append_cigar(r, ez->n_cigar, ez->cigar); mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar); - r->p->score += ez->score; + r->p->score += ez->max; re1 = re + (ez->max_t + 1); qe1 = qe + (ez->max_q + 1); } else re1 = re, qe1 = qe;