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r498: fixed a bug when merging like "4I5I"

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Heng Li
2017-10-10 21:22:37 -04:00
parent 6c78a980b6
commit ca632f907b
3 changed files with 6 additions and 3 deletions
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5
format.c
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@@ -177,12 +177,13 @@ static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_
tmp[j] = "acgtn"[qseq[q_off + j]];
mm_sprintf_lite(s, "+%s", tmp);
q_off += len;
} else if (op == 2 || (op == 3 && len < 4)) {
} else if (op == 2) {
for (j = 0, tmp[len] = 0; j < len; ++j)
tmp[j] = "acgtn"[tseq[t_off + j]];
mm_sprintf_lite(s, "-%s", tmp);
t_off += len;
} else { // op == 3 && len >= 4
} else {
assert(len >= 2);
mm_sprintf_lite(s, "~%c%c%d%c%c", "acgtn"[tseq[t_off]], "acgtn"[tseq[t_off+1]],
len, "acgtn"[tseq[t_off+len-2]], "acgtn"[tseq[t_off+len-1]]);
t_off += len;