From a9cae8c9af8a3e8b9983f146b14b7672a832f463 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 21 Feb 2013 10:39:17 -0500 Subject: [PATCH] minor changes --- bwamem_pair.c | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/bwamem_pair.c b/bwamem_pair.c index 1302414..7dc67fe 100644 --- a/bwamem_pair.c +++ b/bwamem_pair.c @@ -268,13 +268,16 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co // the following assumes no split hits if (z[0] == 0 && z[1] == 0) { // the best hit q_pe = q_pe > q_se[0] + q_se[1]? q_pe : q_se[0] + q_se[1]; + if (q_pe > 60) q_pe = 60; q_se[0] = is_tandem[0]? q_se[0] : q_pe; q_se[1] = is_tandem[1]? q_se[1] : q_pe; extra_flag |= 2; } else { if (o > un) { // then move the pair - q_se[0] = z[0] == 0? q_se[0] : 0; - q_se[1] = z[1] == 0? q_se[1] : 0; + int tmp[2]; + tmp[0] = q_se[0]; tmp[1] = q_se[1]; + q_se[0] = z[0] == 0? q_se[0] : tmp[1] < q_pe? tmp[1] : q_pe; + q_se[1] = z[1] == 0? q_se[1] : tmp[0] < q_pe? tmp[0] : q_pe; if (q_se[0] == 0) q_se[0] = q_se[1]; if (q_se[1] == 0) q_se[1] = q_se[0]; } else { // the unpaired alignment is much better