INNER CODE UNIT · C
tmp
lh3/ksw2 · ksw2_extd.c:37
tmp = -(gapoe + gape * j) > -(gapoe2 + gape2 * j)? -(gapoe + gape * j) : -(gapoe2 + gape2 * j);
eh[j].e = tmp - gapoe;
eh[j].e2 = tmp - gapoe2;
}
for (; j <= qlen; ++j) eh[j].h = eh[j].e = eh[j].e2 = KSW_NEG_INF; // everything is -inf outside the band
// DP loop
for (i = 0; i < tlen; ++i) { // target sequence is in the outer loop
int32_t f, f2, h1, st, en, max = KSW_NEG_INF, tmp;
int8_t *q = &qp[target[i] * qlen];
st = i > w? i - w : 0;
en = i + w < qlen - 1? i + w : qlen - 1;
tmp = -(gapoe + gape * i) > -(gapoe2 + gape2 * i)? -(gapoe + gape * i) : -(gapoe2 + gape2 * i);
h1 = st > 0? KSW_NEG_INF : tmp;
f = st > 0? KSW_NEG_INF : tmp - gapoe;
f2 = st > 0? KSW_NEG_INF : tmp - gapoe2;
if (!with_cigar) {
for (j = st; j <= en; ++j) {