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exclude identical hits

This commit is contained in:
Heng Li 2013-02-08 14:18:39 -05:00
parent 1bf1a674a8
commit 057b292dde
1 changed files with 8 additions and 1 deletions
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9
bwamem.c
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@ -306,7 +306,7 @@ int mem_chain_flt(const mem_opt_t *opt, int n_chn, mem_chain_t *chains)
return n;
}
#define alnreg_lt(a, b) ((a).score > (b).score)
#define alnreg_lt(a, b) ((a).score > (b).score || ((a).score == (b).score && ((a).rb < (b).rb || ((a).rb == (b).rb && (a).qb < (b).qb))))
KSORT_INIT(mem_ar, mem_alnreg_t, alnreg_lt)
int mem_choose_alnreg_se(const mem_opt_t *opt, int n, mem_alnreg_t *a)
@ -314,6 +314,13 @@ int mem_choose_alnreg_se(const mem_opt_t *opt, int n, mem_alnreg_t *a)
int i, j, m;
if (n <= 1) return n;
ks_introsort(mem_ar, n, a);
for (i = 1; i < n; ++i) { // mark identical hits
if (a[i].score == a[i-1].score && a[i].rb == a[i-1].rb && a[i].qb == a[i-1].qb)
a[i].score = 0;
}
for (i = 1, m = 1; i < n; ++i) // exclude identical hits
if (a[i].score > 0) a[m++] = a[i];
n = m;
for (i = 0; i < n; ++i) a[i].sub = 0;
for (i = 1, m = 1; i < n; ++i) {
for (j = 0; j < m; ++j) {