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r92: fixed a bug for overlapping alignment

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On the PBcR example E. coli reads, miniasm gives one circular unitig.
This commit is contained in:
Heng Li
2017-06-27 22:03:31 -04:00
parent 51057ab673
commit cdc2a1e29f
3 changed files with 6 additions and 3 deletions
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mmpriv.h
+2
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@@ -1,6 +1,7 @@
#ifndef MMPRIV2_H
#define MMPRIV2_H
#include <assert.h>
#include "minimap.h"
#include "bseq.h"
@@ -41,6 +42,7 @@ static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a)
int32_t k = r->as;
r->rev = a[k].x>>63;
r->rid = a[k].x<<1>>33;
assert(r->rid != 0x7fffffff);
r->rs = (int32_t)a[k].x + 1 > (int32_t)(a[k].y>>32)? (int32_t)a[k].x + 1 - (int32_t)(a[k].y>>32) : 0;
r->re = (int32_t)a[k + r->cnt - 1].x + 1;
if (!r->rev) {