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pass BED regions to extd2; not tested

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Heng Li
2018-09-17 12:31:42 -04:00
parent 2b653ecda3
commit d01369ec47
6 changed files with 40 additions and 22 deletions
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index.c
+16 -1
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@@ -134,7 +134,7 @@ int mm_idx_name2id(const mm_idx_t *mi, const char *name)
return k == kh_end(h)? -1 : kh_val(h, k);
}
int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq)
int mm_idx_getseq2(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq, int8_t *b)
{
uint64_t i, st1, en1;
if (rid >= mi->n_seq || st >= mi->seq[rid].len) return -1;
@@ -143,9 +143,24 @@ int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, ui
en1 = mi->seq[rid].offset + en;
for (i = st1; i < en1; ++i)
seq[i - st1] = mm_seq4_get(mi->S, i);
if (b && mi->R) {
uint32_t i, z;
memset(b, 0, en - st);
z = mm_idx_bed_query(mi, (uint64_t)rid << 32 | st);
for (i = z + 1; i < mi->n_R; ++i) {
uint32_t j, rr, rs, re;
rr = mi->R[i].x >> 32, rs = (uint32_t)mi->R[i].x, re = mi->R[i].end;
if (rr != rid || rs >= en) break;
assert(rs >= st);
for (j = rs; j < re; ++j)
b[j - st] = 1;
}
}
return en - st;
}
int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq) { return mm_idx_getseq2(mi, rid, st, en, seq, 0); }
int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
{
int i;