From ebbe9c1eb878eda542e4426f616d453eb890f9d8 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 28 Jul 2017 14:06:56 -0400 Subject: [PATCH] r219: fixed a bug caused by skipping tandem seeds --- align.c | 2 +- main.c | 2 +- misc/mapstat.js | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/align.c b/align.c index 93c8371..7f53a68 100644 --- a/align.c +++ b/align.c @@ -298,7 +298,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int assert(qs1 >= 0 && rs1 >= 0); for (i = 1; i < cnt1; ++i) { // gap filling - if (a[as1+i].y & (MM_SEED_IGNORE|MM_SEED_TANDEM)) continue; + if ((a[as1+i].y & (MM_SEED_IGNORE|MM_SEED_TANDEM)) && i != cnt1 - 1) 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)) { diff --git a/main.c b/main.c index 0c59795..9f69faf 100644 --- a/main.c +++ b/main.c @@ -8,7 +8,7 @@ #include "minimap.h" #include "mmpriv.h" -#define MM_VERSION "2.0-r218-dirty" +#define MM_VERSION "2.0-r219-dirty" void liftrlimit() { diff --git a/misc/mapstat.js b/misc/mapstat.js index dfd1f3b..2f80bb4 100644 --- a/misc/mapstat.js +++ b/misc/mapstat.js @@ -144,7 +144,7 @@ while (file.readline(buf) >= 0) { } if (n_cigar > 65535) ++n_cigar_64k; if (ql + sclip != aqlen) - warn("WARNING: aligned query length is inconsistent with CIGAR at line " + lineno); + warn("WARNING: aligned query length is inconsistent with CIGAR at line " + lineno + " (" + (ql+sclip) + " != " + aqlen + ")"); if (atlen != null && atlen != tl) warn("WARNING: aligned reference length is inconsistent with CIGAR at line " + lineno); if (is_sam) {