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clean bill from valgrind

This commit is contained in:
Heng Li 2013-02-20 20:26:57 -05:00
parent 5626fe29b7
commit ea8f4f4d34
3 changed files with 8 additions and 5 deletions
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5
bwamem.c
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@ -363,7 +363,10 @@ int mem_sort_and_dedup(int n, mem_alnreg_t *a)
a[i].qe = a[i].qb; a[i].qe = a[i].qb;
} }
for (i = 1, m = 1; i < n; ++i) // exclude identical hits 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; return m;
} }

2
bwamem_pair.c
View File

@ -153,7 +153,7 @@ int mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const me
} }
++n; ++n;
} }
if (rev == 0) free(rev); if (rev) free(rev);
free(ref); free(ref);
} }
return n; return n;

6
ksw.c
View File

@ -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 == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) {
if (*n_cigar == *m_cigar) { if (*n_cigar == *m_cigar) {
*m_cigar = *m_cigar? (*m_cigar)<<1 : 4; *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; cigar[(*n_cigar)++] = len<<4 | op;
} else cigar[(*n_cigar)-1] += len<<4; } 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 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; 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 (i >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, i + 1);
if (k >= 0) push_cigar(&n_cigar, &m_cigar, cigar, 1, k + 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 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; tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
*n_cigar_ = n_cigar, *cigar_ = cigar; *n_cigar_ = n_cigar, *cigar_ = cigar;