From ca632f907b900d68a7f80a398fb29599c1367393 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 10 Oct 2017 21:22:37 -0400
Subject: [PATCH] r498: fixed a bug when merging like "4I5I"

---
 align.c  | 2 ++
 format.c | 5 +++--
 main.c   | 2 +-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/align.c b/align.c
index 6046131..9b3e62b 100644
--- a/align.c
+++ b/align.c
@@ -105,6 +105,7 @@ static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq,
 		for (k = l = 0; k < p->n_cigar; ++k) // merge two adjacent operations if they are the same
 			if (k == p->n_cigar - 1 || (p->cigar[k]&0xf) != (p->cigar[k+1]&0xf))
 				p->cigar[l++] = p->cigar[k];
+			else p->cigar[k+1] += p->cigar[k]>>4<<4; // add length to the next CIGAR operator
 		p->n_cigar = l;
 	}
 	if ((p->cigar[0]&0xf) == 1 || (p->cigar[0]&0xf) == 2) { // get rid of leading I or D
@@ -157,6 +158,7 @@ static void mm_update_extra(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *ts
 		}
 	}
 	p->dp_max = max;
+	assert(qoff == r->qe - r->qs && toff == r->re - r->rs);
 }
 
 static void mm_append_cigar(mm_reg1_t *r, uint32_t n_cigar, uint32_t *cigar) // TODO: this calls the libc realloc()
diff --git a/format.c b/format.c
index ef12397..d72e2d1 100644
--- a/format.c
+++ b/format.c
@@ -177,12 +177,13 @@ static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_
 				tmp[j] = "acgtn"[qseq[q_off + j]];
 			mm_sprintf_lite(s, "+%s", tmp);
 			q_off += len;
-		} else if (op == 2 || (op == 3 && len < 4)) {
+		} else if (op == 2) {
 			for (j = 0, tmp[len] = 0; j < len; ++j)
 				tmp[j] = "acgtn"[tseq[t_off + j]];
 			mm_sprintf_lite(s, "-%s", tmp);
 			t_off += len;
-		} else { // op == 3 && len >= 4
+		} else {
+			assert(len >= 2);
 			mm_sprintf_lite(s, "~%c%c%d%c%c", "acgtn"[tseq[t_off]], "acgtn"[tseq[t_off+1]],
 				len, "acgtn"[tseq[t_off+len-2]], "acgtn"[tseq[t_off+len-1]]);
 			t_off += len;
diff --git a/main.c b/main.c
index d59545e..a03c5c8 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.2-r497-dirty"
+#define MM_VERSION "2.2-r498-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>