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fixed a boundary bug in global() 

Actually global2() is correct. It is global() that is wrong.
This commit is contained in:
Heng Li 2017-06-16 12:47:09 -04:00
parent 7d33acbccc
commit 359b829350
1 changed files with 4 additions and 4 deletions
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8
ksw2.c
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@ -175,9 +175,9 @@ int ksw_global(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t
}
// fill the first row
eh[0].h = 0, eh[0].e = -gapoe - gapoe; // -gapoe*2: one deletion followed by one insertion
eh[0].h = 0, eh[0].e = -gapoe - gapo;
for (j = 1; j <= qlen && j <= w; ++j)
eh[j].h = -(gapo + gape * j), eh[j].e = eh[j-1].e - gape;
eh[j].h = -(gapo + gape * j), eh[j].e = -(gapoe + gapo + gape * j);
for (; j <= qlen; ++j) eh[j].h = eh[j].e = NEG_INF; // everything is -inf outside the band
// DP loop
@ -191,8 +191,8 @@ int ksw_global(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t
st = i > w? i - w : 0;
en = i + w + 1 < qlen? i + w + 1 : qlen;
#endif
h1 = st > 0? NEG_INF : -gapoe - gape * (i + 1);
f = st > 0? NEG_INF : -gapoe - gapoe - gape * i; // similarly, -gapoe*2: one del followed by one ins
h1 = st > 0? NEG_INF : -(gapo + gape * i);
f = st > 0? NEG_INF : -(gapoe + gapo + gape * i);
off[i] = st;
if (n_cigar_ && cigar_) {
uint8_t *zi = &z[(long)i * n_col];