From ea8f4f4d34b05be0c3a821c9eede57fae39c5477 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 20 Feb 2013 20:26:57 -0500
Subject: [PATCH] clean bill from valgrind

---
 bwamem.c      | 5 ++++-
 bwamem_pair.c | 2 +-
 ksw.c         | 6 +++---
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index f9415b2..f0e1a29 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -363,7 +363,10 @@ int mem_sort_and_dedup(int n, mem_alnreg_t *a)
 			a[i].qe = a[i].qb;
 	}
 	for (i = 1, m = 1; i < n; ++i) // exclude identical hits
-		if (a[i].qe > a[i].qb) a[m++] = a[i];
+		if (a[i].qe > a[i].qb) {
+			if (m != i) a[m++] = a[i];
+			else ++m;
+		}
 	return m;
 }
 
diff --git a/bwamem_pair.c b/bwamem_pair.c
index dc46f44..092eee2 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -153,7 +153,7 @@ int mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const me
 			}
 			++n;
 		}
-		if (rev == 0) free(rev);
+		if (rev) free(rev);
 		free(ref);
 	}
 	return n;
diff --git a/ksw.c b/ksw.c
index 8d741a6..742fec9 100644
--- a/ksw.c
+++ b/ksw.c
@@ -447,7 +447,7 @@ static inline uint32_t *push_cigar(int *n_cigar, int *m_cigar, uint32_t *cigar,
 	if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) {
 		if (*n_cigar == *m_cigar) {
 			*m_cigar = *m_cigar? (*m_cigar)<<1 : 4;
-			cigar = realloc(cigar, (*m_cigar) << 4);
+			cigar = realloc(cigar, (*m_cigar) << 2);
 		}
 		cigar[(*n_cigar)++] = len<<4 | op;
 	} else cigar[(*n_cigar)-1] += len<<4;
@@ -520,8 +520,8 @@ int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
 			else if (which == 1) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, 1), --i;
 			else                 cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, 1), --k;
 		}
-		if (i >= 0) push_cigar(&n_cigar, &m_cigar, cigar, 2, i + 1);
-		if (k >= 0) push_cigar(&n_cigar, &m_cigar, cigar, 1, k + 1);
+		if (i >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, i + 1);
+		if (k >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, k + 1);
 		for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
 			tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
 		*n_cigar_ = n_cigar, *cigar_ = cigar;