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add break condition to making cigar string #362

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add break condition to making cigar string #362

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c49ba44
add break condition to making cigar string
gayoung-MetisX Jul 22, 2022
2855ed8
fix condition
gayoung-MetisX Jul 26, 2022
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6 changes: 5 additions & 1 deletion ksw.c
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Original file line number Diff line number Diff line change
Expand Up @@ -590,7 +590,11 @@ int ksw_global2(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
uint32_t *cigar = 0, tmp;
i = tlen - 1; k = (i + w + 1 < qlen? i + w + 1 : qlen) - 1; // (i,k) points to the last cell
while (i >= 0 && k >= 0) {
which = z[(long)i * n_col + (k - (i > w? i - w : 0))] >> (which<<1) & 3;
int j_beg = i > w? i - w : 0;
int j_end = i + w + 1 < qlen? i + w + 1 : qlen;
j = (k - j_beg);
if (j >= (j_end-j_beg)) break;
which = z[(long)i * n_col + j] >> (which<<1) & 3;
if (which == 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 0, 1), --i, --k;
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;
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